Starting phenix.real_space_refine on Mon Jul 28 05:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6p_38994/07_2025/8y6p_38994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6p_38994/07_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_38994/07_2025/8y6p_38994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6p_38994/07_2025/8y6p_38994.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6p_38994/07_2025/8y6p_38994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6p_38994/07_2025/8y6p_38994_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 6.60, per 1000 atoms: 0.66 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: 3.46 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.86 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: 4.54 Time building geometry restraints manager: 3.95 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: 1.390 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- 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 : 19.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (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 TRP 0.045 0.002 TRP Q 341 HIS 0.004 0.001 HIS Q 593 PHE 0.010 0.001 PHE Q1349 TYR 0.056 0.002 TYR Q1366 ARG 0.009 0.001 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.16226 ( 360) hydrogen bonds : angle 6.89999 ( 1020) covalent geometry : bond 0.00409 (10191) covalent geometry : angle 0.90351 (13809) *********************** 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 : 1.161 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: 0.6747 (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: 0.8021 (m-10) outliers start: 15 outliers final: 8 residues processed: 185 average time/residue: 0.2345 time to fit residues: 60.6728 Evaluate side-chains 166 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 103 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085503 restraints weight = 30285.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087982 restraints weight = 18039.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089712 restraints weight = 12478.251| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10191 Z= 0.163 Angle : 0.711 9.739 13809 Z= 0.364 Chirality : 0.047 0.234 1578 Planarity : 0.006 0.090 1739 Dihedral : 6.609 51.026 1339 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.05 % Favored : 91.96 % Rotamer: Outliers : 5.19 % Allowed : 24.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1206 helix: -0.19 (0.31), residues: 307 sheet: 0.62 (0.28), residues: 345 loop : -1.63 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 341 HIS 0.004 0.001 HIS Q1013 PHE 0.018 0.002 PHE Q 523 TYR 0.052 0.002 TYR Q 527 ARG 0.004 0.001 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 360) hydrogen bonds : angle 5.84813 ( 1020) covalent geometry : bond 0.00375 (10191) covalent geometry : angle 0.71130 (13809) *********************** 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 224 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 283 ILE cc_start: 0.8845 (mm) cc_final: 0.8614 (mm) REVERT: Q 323 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6161 (mmt90) REVERT: Q 366 ARG cc_start: 0.8393 (tpt-90) cc_final: 0.7856 (tpp-160) REVERT: Q 660 PHE cc_start: 0.8139 (p90) cc_final: 0.7875 (p90) REVERT: Q 911 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: Q 1024 SER cc_start: 0.9126 (t) cc_final: 0.8797 (t) REVERT: Q 1156 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8296 (tp) REVERT: Q 1361 ASP cc_start: 0.8733 (p0) cc_final: 0.8494 (p0) outliers start: 58 outliers final: 30 residues processed: 206 average time/residue: 0.2275 time to fit residues: 65.8909 Evaluate side-chains 183 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 158 THR 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 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 453 PHE 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 605 LEU Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 911 PHE Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1123 VAL 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 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 85 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 0.0370 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 239 ASN Q 516 ASN 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 = 0.3699 r_free = 0.3699 target = 0.104187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087629 restraints weight = 30672.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090346 restraints weight = 17145.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092286 restraints weight = 11450.583| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10191 Z= 0.117 Angle : 0.669 8.467 13809 Z= 0.336 Chirality : 0.045 0.224 1578 Planarity : 0.005 0.085 1739 Dihedral : 5.986 52.104 1332 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 1.08 % Allowed : 6.80 % Favored : 92.12 % Rotamer: Outliers : 4.29 % Allowed : 23.88 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1206 helix: 0.05 (0.32), residues: 307 sheet: 0.78 (0.29), residues: 333 loop : -1.62 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Q 341 HIS 0.006 0.001 HIS Q 480 PHE 0.012 0.001 PHE Q 523 TYR 0.051 0.002 TYR Q 527 ARG 0.010 0.001 ARG Q 82 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 360) hydrogen bonds : angle 5.54280 ( 1020) covalent geometry : bond 0.00260 (10191) covalent geometry : angle 0.66935 (13809) *********************** 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 223 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 85 TYR cc_start: 0.7406 (m-80) cc_final: 0.7202 (m-80) REVERT: Q 323 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.5950 (mmt90) REVERT: Q 366 ARG cc_start: 0.8467 (tpt-90) cc_final: 0.8061 (tpp-160) REVERT: Q 516 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8254 (t0) REVERT: Q 660 PHE cc_start: 0.8002 (p90) cc_final: 0.7790 (p90) REVERT: Q 1024 SER cc_start: 0.9191 (t) cc_final: 0.8883 (t) REVERT: Q 1361 ASP cc_start: 0.8746 (p0) cc_final: 0.8427 (p0) outliers start: 48 outliers final: 27 residues processed: 207 average time/residue: 0.2379 time to fit residues: 67.4701 Evaluate side-chains 182 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 258 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 411 VAL 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 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 516 ASN 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 743 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 1046 ASP Chi-restraints excluded: chain Q residue 1123 VAL 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 44 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 593 HIS Q 952 HIS Q1368 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.083890 restraints weight = 30742.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086544 restraints weight = 17200.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088329 restraints weight = 11509.514| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10191 Z= 0.182 Angle : 0.713 15.216 13809 Z= 0.359 Chirality : 0.046 0.206 1578 Planarity : 0.005 0.082 1739 Dihedral : 5.868 51.028 1328 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.46 % Favored : 91.54 % Rotamer: Outliers : 5.55 % Allowed : 23.26 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1206 helix: 0.02 (0.31), residues: 311 sheet: 0.71 (0.29), residues: 336 loop : -1.67 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 341 HIS 0.004 0.001 HIS Q 757 PHE 0.014 0.001 PHE Q 494 TYR 0.051 0.002 TYR Q 527 ARG 0.005 0.001 ARG Q 322 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 360) hydrogen bonds : angle 5.59488 ( 1020) covalent geometry : bond 0.00415 (10191) covalent geometry : angle 0.71282 (13809) *********************** 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: 62 poor density : 160 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 323 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.6254 (mmt90) REVERT: Q 516 ASN cc_start: 0.8812 (t0) cc_final: 0.8503 (t0) REVERT: Q 660 PHE cc_start: 0.8095 (p90) cc_final: 0.7888 (p90) REVERT: Q 775 LEU cc_start: 0.7958 (tt) cc_final: 0.7741 (tp) REVERT: Q 1024 SER cc_start: 0.9298 (t) cc_final: 0.9033 (t) REVERT: Q 1156 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8260 (tp) REVERT: Q 1205 MET cc_start: 0.8401 (mpp) cc_final: 0.8080 (mtt) REVERT: Q 1361 ASP cc_start: 0.8727 (p0) cc_final: 0.8517 (p0) outliers start: 62 outliers final: 36 residues processed: 204 average time/residue: 0.2342 time to fit residues: 66.9480 Evaluate side-chains 183 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE 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 258 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 440 HIS Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 475 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 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 1046 ASP Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1072 SER Chi-restraints excluded: chain Q residue 1123 VAL 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 1222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 751 GLN Q 952 HIS Q1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080778 restraints weight = 30957.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083389 restraints weight = 17584.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085115 restraints weight = 11878.387| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10191 Z= 0.239 Angle : 0.761 10.923 13809 Z= 0.387 Chirality : 0.048 0.193 1578 Planarity : 0.006 0.082 1739 Dihedral : 6.223 59.642 1327 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.29 % Favored : 89.72 % Rotamer: Outliers : 6.80 % Allowed : 23.43 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 1206 helix: -0.27 (0.30), residues: 314 sheet: 0.60 (0.29), residues: 329 loop : -1.90 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 341 HIS 0.006 0.001 HIS Q 480 PHE 0.022 0.002 PHE Q 494 TYR 0.062 0.003 TYR Q 527 ARG 0.005 0.001 ARG Q 322 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 360) hydrogen bonds : angle 5.82033 ( 1020) covalent geometry : bond 0.00544 (10191) covalent geometry : angle 0.76135 (13809) *********************** 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 225 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 149 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 72 MET cc_start: 0.7996 (mmm) cc_final: 0.7552 (mmm) REVERT: Q 85 TYR cc_start: 0.7593 (m-80) cc_final: 0.7158 (m-80) REVERT: Q 89 MET cc_start: 0.7020 (mmt) cc_final: 0.6704 (mmt) REVERT: Q 159 TRP cc_start: 0.3329 (OUTLIER) cc_final: 0.2876 (m100) REVERT: Q 323 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.6299 (mmt90) REVERT: Q 576 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: Q 681 TRP cc_start: 0.8197 (m100) cc_final: 0.7922 (m-10) REVERT: Q 775 LEU cc_start: 0.8140 (tt) cc_final: 0.7853 (tp) REVERT: Q 990 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8617 (mtmt) REVERT: Q 1013 HIS cc_start: 0.5794 (OUTLIER) cc_final: 0.5251 (t-90) REVERT: Q 1024 SER cc_start: 0.9334 (t) cc_final: 0.9128 (t) REVERT: Q 1361 ASP cc_start: 0.8937 (p0) cc_final: 0.8314 (p0) outliers start: 76 outliers final: 47 residues processed: 204 average time/residue: 0.2403 time to fit residues: 69.5553 Evaluate side-chains 189 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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 258 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 318 THR Chi-restraints excluded: chain Q residue 319 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 437 TYR Chi-restraints excluded: chain Q residue 444 VAL Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 475 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 501 ILE Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 562 LEU Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 579 LYS 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 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 1080 VAL Chi-restraints excluded: chain Q residue 1123 VAL 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 40 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.0870 chunk 73 optimal weight: 9.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 222 HIS ** Q 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 927 GLN Q 952 HIS Q1179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084485 restraints weight = 30517.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087126 restraints weight = 17377.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089007 restraints weight = 11814.144| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10191 Z= 0.123 Angle : 0.718 10.573 13809 Z= 0.353 Chirality : 0.046 0.274 1578 Planarity : 0.005 0.089 1739 Dihedral : 5.738 50.129 1325 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.55 % Favored : 91.46 % Rotamer: Outliers : 4.65 % Allowed : 26.03 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1206 helix: -0.07 (0.31), residues: 313 sheet: 0.77 (0.29), residues: 328 loop : -1.80 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 589 HIS 0.004 0.001 HIS Q 222 PHE 0.015 0.001 PHE Q 19 TYR 0.053 0.002 TYR Q 527 ARG 0.004 0.000 ARG Q 895 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 360) hydrogen bonds : angle 5.51414 ( 1020) covalent geometry : bond 0.00280 (10191) covalent geometry : angle 0.71822 (13809) *********************** 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 212 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6967 (tm-30) REVERT: Q 85 TYR cc_start: 0.7588 (m-80) cc_final: 0.7235 (m-80) REVERT: Q 283 ILE cc_start: 0.8676 (mm) cc_final: 0.8413 (mm) REVERT: Q 323 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6357 (mmt90) REVERT: Q 515 LEU cc_start: 0.8908 (mp) cc_final: 0.8619 (mp) REVERT: Q 516 ASN cc_start: 0.8796 (t0) cc_final: 0.8421 (t0) REVERT: Q 678 TRP cc_start: 0.8407 (m100) cc_final: 0.8082 (m100) REVERT: Q 681 TRP cc_start: 0.8188 (m100) cc_final: 0.7966 (m-10) REVERT: Q 1013 HIS cc_start: 0.5664 (OUTLIER) cc_final: 0.5143 (t-90) REVERT: Q 1024 SER cc_start: 0.9306 (t) cc_final: 0.9083 (t) REVERT: Q 1205 MET cc_start: 0.8169 (mtt) cc_final: 0.7645 (mtm) REVERT: Q 1361 ASP cc_start: 0.8823 (p0) cc_final: 0.8212 (p0) outliers start: 52 outliers final: 30 residues processed: 197 average time/residue: 0.2307 time to fit residues: 63.8434 Evaluate side-chains 184 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain Q residue 149 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 265 THR 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 449 ILE Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 579 LYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3619 r_free = 0.3619 target = 0.099856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083251 restraints weight = 31130.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085920 restraints weight = 17437.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087737 restraints weight = 11685.914| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10191 Z= 0.153 Angle : 0.713 8.854 13809 Z= 0.355 Chirality : 0.046 0.224 1578 Planarity : 0.005 0.082 1739 Dihedral : 5.699 48.361 1325 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.55 % Favored : 91.54 % Rotamer: Outliers : 4.65 % Allowed : 26.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1206 helix: -0.04 (0.31), residues: 313 sheet: 0.66 (0.29), residues: 327 loop : -1.82 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP Q 341 HIS 0.003 0.001 HIS Q 343 PHE 0.024 0.001 PHE Q1155 TYR 0.061 0.002 TYR Q 527 ARG 0.005 0.001 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 360) hydrogen bonds : angle 5.54951 ( 1020) covalent geometry : bond 0.00361 (10191) covalent geometry : angle 0.71250 (13809) *********************** 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 200 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 85 TYR cc_start: 0.7546 (m-80) cc_final: 0.7192 (m-80) REVERT: Q 283 ILE cc_start: 0.8711 (mm) cc_final: 0.8468 (mm) REVERT: Q 323 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6432 (mmt90) REVERT: Q 368 MET cc_start: 0.8944 (tpp) cc_final: 0.8506 (mmm) REVERT: Q 678 TRP cc_start: 0.8411 (m100) cc_final: 0.8038 (m100) REVERT: Q 751 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8460 (mp10) REVERT: Q 990 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8550 (mtmt) REVERT: Q 1013 HIS cc_start: 0.5712 (OUTLIER) cc_final: 0.5209 (t-90) REVERT: Q 1024 SER cc_start: 0.9346 (t) cc_final: 0.9115 (t) REVERT: Q 1163 ILE cc_start: 0.9001 (mt) cc_final: 0.8786 (mt) REVERT: Q 1361 ASP cc_start: 0.8785 (p0) cc_final: 0.8464 (p0) REVERT: Q 1363 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8829 (mm-30) outliers start: 52 outliers final: 41 residues processed: 187 average time/residue: 0.2299 time to fit residues: 60.3147 Evaluate side-chains 187 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 79 GLU Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 148 LEU 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 318 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 326 ILE Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 411 VAL 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 579 LYS Chi-restraints excluded: chain Q residue 595 ARG 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 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 1040 ILE 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 1360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 340 ASN Q 516 ASN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.082458 restraints weight = 30907.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084855 restraints weight = 18754.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086520 restraints weight = 13149.518| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10191 Z= 0.182 Angle : 0.749 17.301 13809 Z= 0.369 Chirality : 0.047 0.230 1578 Planarity : 0.005 0.082 1739 Dihedral : 5.799 49.124 1325 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.21 % Favored : 90.88 % Rotamer: Outliers : 5.19 % Allowed : 26.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1206 helix: -0.07 (0.31), residues: 314 sheet: 0.54 (0.29), residues: 323 loop : -1.86 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Q 207 HIS 0.004 0.001 HIS Q 343 PHE 0.021 0.002 PHE Q1155 TYR 0.060 0.002 TYR Q 527 ARG 0.007 0.001 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 360) hydrogen bonds : angle 5.63217 ( 1020) covalent geometry : bond 0.00422 (10191) covalent geometry : angle 0.74939 (13809) *********************** 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 207 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 72 MET cc_start: 0.8131 (mmm) cc_final: 0.7904 (mtt) REVERT: Q 85 TYR cc_start: 0.7557 (m-80) cc_final: 0.7253 (m-80) REVERT: Q 283 ILE cc_start: 0.8833 (mm) cc_final: 0.8588 (mm) REVERT: Q 323 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.6668 (mmt90) REVERT: Q 368 MET cc_start: 0.8962 (tpp) cc_final: 0.8540 (mmm) REVERT: Q 647 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6042 (t0) REVERT: Q 678 TRP cc_start: 0.8497 (m100) cc_final: 0.8132 (m100) REVERT: Q 751 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8351 (mp10) REVERT: Q 775 LEU cc_start: 0.8068 (tt) cc_final: 0.7743 (tp) REVERT: Q 1013 HIS cc_start: 0.5880 (OUTLIER) cc_final: 0.5454 (t-90) REVERT: Q 1024 SER cc_start: 0.9338 (t) cc_final: 0.9134 (t) REVERT: Q 1263 MET cc_start: 0.8881 (mmm) cc_final: 0.8641 (mtt) REVERT: Q 1361 ASP cc_start: 0.8830 (p0) cc_final: 0.8198 (p0) outliers start: 58 outliers final: 45 residues processed: 192 average time/residue: 0.2312 time to fit residues: 61.6796 Evaluate side-chains 190 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 79 GLU 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 318 THR Chi-restraints excluded: chain Q residue 319 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 326 ILE Chi-restraints excluded: chain Q residue 340 ASN Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 437 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 516 ASN Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 579 LYS 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 642 THR Chi-restraints excluded: chain Q residue 647 ASP 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 933 THR Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1013 HIS 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 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Chi-restraints excluded: chain Q residue 1360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 69 optimal weight: 0.0040 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 61 optimal weight: 9.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 340 ASN Q 516 ASN ** Q 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084712 restraints weight = 30613.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087128 restraints weight = 18798.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088845 restraints weight = 13340.769| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10191 Z= 0.122 Angle : 0.746 16.875 13809 Z= 0.361 Chirality : 0.046 0.258 1578 Planarity : 0.005 0.084 1739 Dihedral : 5.687 49.058 1325 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.21 % Favored : 91.96 % Rotamer: Outliers : 4.11 % Allowed : 27.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1206 helix: -0.03 (0.31), residues: 315 sheet: 0.54 (0.29), residues: 330 loop : -1.79 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 207 HIS 0.005 0.001 HIS Q 343 PHE 0.018 0.001 PHE Q1155 TYR 0.061 0.002 TYR Q 527 ARG 0.010 0.000 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 360) hydrogen bonds : angle 5.48979 ( 1020) covalent geometry : bond 0.00282 (10191) covalent geometry : angle 0.74624 (13809) *********************** 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: 46 poor density : 153 time to evaluate : 1.251 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: 0.6777 (tm-30) REVERT: Q 85 TYR cc_start: 0.7420 (m-80) cc_final: 0.7102 (m-80) REVERT: Q 283 ILE cc_start: 0.8743 (mm) cc_final: 0.8543 (mm) REVERT: Q 298 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8881 (mtmm) REVERT: Q 323 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6541 (mmt90) REVERT: Q 329 GLU cc_start: 0.7937 (tt0) cc_final: 0.7351 (tt0) REVERT: Q 368 MET cc_start: 0.8903 (tpp) cc_final: 0.8507 (mmm) REVERT: Q 660 PHE cc_start: 0.7958 (p90) cc_final: 0.7724 (p90) REVERT: Q 775 LEU cc_start: 0.8087 (tt) cc_final: 0.7776 (tp) REVERT: Q 1013 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5625 (t-90) REVERT: Q 1024 SER cc_start: 0.9278 (t) cc_final: 0.9022 (t) REVERT: Q 1263 MET cc_start: 0.8960 (mmm) cc_final: 0.8749 (mtt) REVERT: Q 1361 ASP cc_start: 0.8851 (p0) cc_final: 0.8528 (p0) outliers start: 46 outliers final: 33 residues processed: 185 average time/residue: 0.2363 time to fit residues: 61.4405 Evaluate side-chains 179 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 79 GLU 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 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 319 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 447 TYR Chi-restraints excluded: chain Q residue 449 ILE 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 579 LYS Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 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 933 THR Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Chi-restraints excluded: chain Q residue 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 30 optimal weight: 0.0370 chunk 60 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.1064 ------------------------------------------------------------------------------- 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 699 ASN ** 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 = 0.3812 r_free = 0.3812 target = 0.108460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092367 restraints weight = 31505.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094945 restraints weight = 18793.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096761 restraints weight = 13094.296| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10191 Z= 0.138 Angle : 0.746 16.230 13809 Z= 0.363 Chirality : 0.046 0.246 1578 Planarity : 0.005 0.083 1739 Dihedral : 5.624 47.519 1325 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.30 % Favored : 91.87 % Rotamer: Outliers : 3.31 % Allowed : 28.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1206 helix: 0.02 (0.31), residues: 314 sheet: 0.59 (0.29), residues: 327 loop : -1.85 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Q 207 HIS 0.006 0.001 HIS Q 480 PHE 0.019 0.001 PHE Q1155 TYR 0.064 0.002 TYR Q 527 ARG 0.013 0.001 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 360) hydrogen bonds : angle 5.48939 ( 1020) covalent geometry : bond 0.00327 (10191) covalent geometry : angle 0.74645 (13809) ********************** 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 186 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 85 TYR cc_start: 0.7426 (m-80) cc_final: 0.7026 (m-80) REVERT: Q 283 ILE cc_start: 0.8891 (mm) cc_final: 0.8684 (mm) REVERT: Q 323 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.6668 (mmt90) REVERT: Q 329 GLU cc_start: 0.7650 (tt0) cc_final: 0.6948 (tt0) REVERT: Q 368 MET cc_start: 0.8838 (tpp) cc_final: 0.8548 (mmm) REVERT: Q 595 ARG cc_start: 0.6009 (ptp90) cc_final: 0.4930 (mmt-90) REVERT: Q 660 PHE cc_start: 0.7854 (p90) cc_final: 0.7636 (p90) REVERT: Q 1013 HIS cc_start: 0.6133 (OUTLIER) cc_final: 0.5834 (t-90) REVERT: Q 1024 SER cc_start: 0.9226 (t) cc_final: 0.9013 (t) REVERT: Q 1263 MET cc_start: 0.8509 (mmm) cc_final: 0.8155 (mtt) REVERT: Q 1361 ASP cc_start: 0.8749 (p0) cc_final: 0.8449 (p0) outliers start: 37 outliers final: 32 residues processed: 176 average time/residue: 0.2210 time to fit residues: 55.4901 Evaluate side-chains 178 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 79 GLU 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 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 319 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 449 ILE Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 579 LYS Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 680 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 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 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Chi-restraints excluded: chain Q residue 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 0.0010 chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 516 ASN ** Q 699 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.108319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092205 restraints weight = 31751.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094856 restraints weight = 18723.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096592 restraints weight = 12906.203| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10191 Z= 0.126 Angle : 0.748 13.766 13809 Z= 0.364 Chirality : 0.046 0.252 1578 Planarity : 0.005 0.084 1739 Dihedral : 5.602 47.170 1325 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.71 % Favored : 91.63 % Rotamer: Outliers : 3.49 % Allowed : 28.98 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1206 helix: 0.06 (0.31), residues: 314 sheet: 0.60 (0.29), residues: 329 loop : -1.81 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Q 207 HIS 0.005 0.001 HIS Q1232 PHE 0.017 0.001 PHE Q1155 TYR 0.062 0.002 TYR Q 527 ARG 0.013 0.001 ARG Q 595 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 360) hydrogen bonds : angle 5.56833 ( 1020) covalent geometry : bond 0.00294 (10191) covalent geometry : angle 0.74849 (13809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.30 seconds wall clock time: 57 minutes 53.56 seconds (3473.56 seconds total)