Starting phenix.real_space_refine on Sun Aug 4 08:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6p_38994/08_2024/8y6p_38994_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6p_38994/08_2024/8y6p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6p_38994/08_2024/8y6p_38994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6p_38994/08_2024/8y6p_38994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6p_38994/08_2024/8y6p_38994_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6p_38994/08_2024/8y6p_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 Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q GLU 329": "OE1" <-> "OE2" Residue "Q TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 571": "OE1" <-> "OE2" Residue "Q GLU 575": "OE1" <-> "OE2" Residue "Q GLU 900": "OE1" <-> "OE2" Residue "Q GLU 966": "OE1" <-> "OE2" Residue "Q GLU 991": "OE1" <-> "OE2" Residue "Q GLU 1029": "OE1" <-> "OE2" Residue "Q GLU 1055": "OE1" <-> "OE2" Residue "Q GLU 1159": "OE1" <-> "OE2" Residue "Q GLU 1178": "OE1" <-> "OE2" Residue "Q GLU 1182": "OE1" <-> "OE2" Residue "Q GLU 1183": "OE1" <-> "OE2" Residue "Q GLU 1218": "OE1" <-> "OE2" Residue "Q GLU 1230": "OE1" <-> "OE2" Residue "Q GLU 1253": "OE1" <-> "OE2" Residue "Q GLU 1320": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.62, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 3.66 Conformation dependent library (CDL) restraints added in 1.6 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: 1.43 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: 4.04 Time building geometry restraints manager: 4.05 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: 95.48 - 103.23: 65 103.23 - 110.98: 3717 110.98 - 118.73: 4522 118.73 - 126.47: 5345 126.47 - 134.22: 160 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.470 Find NCS groups from input model: 0.090 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- 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= 0.278 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 1.218 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: 0.2304 time to fit residues: 59.2842 Evaluate side-chains 166 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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= 0.241 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 *********************** 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 fitting. rotamer outliers: 58 poor density : 166 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 283 ILE cc_start: 0.8942 (mm) cc_final: 0.8709 (mm) REVERT: Q 323 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.6144 (mmt90) REVERT: Q 366 ARG cc_start: 0.8254 (tpt-90) cc_final: 0.7811 (tpp-160) REVERT: Q 660 PHE cc_start: 0.8081 (p90) cc_final: 0.7816 (p90) REVERT: Q 1024 SER cc_start: 0.9072 (t) cc_final: 0.8765 (t) REVERT: Q 1156 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8274 (tp) REVERT: Q 1263 MET cc_start: 0.8753 (mmm) cc_final: 0.8484 (mtt) REVERT: Q 1361 ASP cc_start: 0.8730 (p0) cc_final: 0.8500 (p0) outliers start: 58 outliers final: 30 residues processed: 206 average time/residue: 0.2264 time to fit residues: 64.8343 Evaluate side-chains 183 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10191 Z= 0.173 Angle : 0.674 7.880 13809 Z= 0.338 Chirality : 0.045 0.221 1578 Planarity : 0.005 0.086 1739 Dihedral : 6.024 51.049 1332 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 1.08 % Allowed : 6.88 % Favored : 92.04 % Rotamer: Outliers : 4.83 % Allowed : 23.43 % Favored : 71.74 % 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: -0.75 (0.25), residues: 1206 helix: 0.09 (0.32), residues: 306 sheet: 0.74 (0.29), residues: 335 loop : -1.64 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Q 341 HIS 0.006 0.001 HIS Q 480 PHE 0.016 0.001 PHE Q 911 TYR 0.055 0.002 TYR Q 527 ARG 0.009 0.001 ARG Q 82 *********************** 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 228 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 323 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.5972 (mmt90) REVERT: Q 366 ARG cc_start: 0.8291 (tpt-90) cc_final: 0.7980 (tpp-160) REVERT: Q 516 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7988 (t0) REVERT: Q 660 PHE cc_start: 0.7912 (p90) cc_final: 0.7701 (p90) REVERT: Q 1024 SER cc_start: 0.9151 (t) cc_final: 0.8887 (t) REVERT: Q 1163 ILE cc_start: 0.9356 (mp) cc_final: 0.9079 (mt) REVERT: Q 1263 MET cc_start: 0.8733 (mmm) cc_final: 0.8518 (mtt) REVERT: Q 1361 ASP cc_start: 0.8757 (p0) cc_final: 0.8431 (p0) outliers start: 54 outliers final: 32 residues processed: 212 average time/residue: 0.2397 time to fit residues: 69.5553 Evaluate side-chains 189 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 411 VAL Chi-restraints excluded: chain Q residue 425 ILE Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 446 HIS 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 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 1040 ILE Chi-restraints excluded: chain Q residue 1046 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 340 ASN Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10191 Z= 0.160 Angle : 0.685 15.453 13809 Z= 0.338 Chirality : 0.045 0.219 1578 Planarity : 0.005 0.091 1739 Dihedral : 5.807 50.449 1330 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.63 % Favored : 92.37 % Rotamer: Outliers : 4.65 % Allowed : 23.35 % Favored : 72.00 % 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: -0.65 (0.26), residues: 1206 helix: 0.04 (0.31), residues: 313 sheet: 0.87 (0.29), residues: 332 loop : -1.54 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 341 HIS 0.004 0.001 HIS Q 480 PHE 0.013 0.001 PHE Q 523 TYR 0.049 0.001 TYR Q 527 ARG 0.004 0.000 ARG Q 82 *********************** 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 225 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6895 (tm-30) REVERT: Q 323 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6082 (mmt90) REVERT: Q 516 ASN cc_start: 0.8314 (t0) cc_final: 0.8076 (t0) REVERT: Q 660 PHE cc_start: 0.7899 (p90) cc_final: 0.7686 (p90) REVERT: Q 919 VAL cc_start: 0.8885 (t) cc_final: 0.8353 (p) REVERT: Q 1024 SER cc_start: 0.9142 (t) cc_final: 0.8855 (t) REVERT: Q 1163 ILE cc_start: 0.9300 (mp) cc_final: 0.8964 (mt) REVERT: Q 1263 MET cc_start: 0.8680 (mmm) cc_final: 0.8441 (mtt) outliers start: 52 outliers final: 28 residues processed: 213 average time/residue: 0.2266 time to fit residues: 66.8418 Evaluate side-chains 187 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 181 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 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 447 TYR 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 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 951 VAL 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 1222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 480 HIS ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Q1368 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10191 Z= 0.286 Angle : 0.717 8.318 13809 Z= 0.364 Chirality : 0.046 0.198 1578 Planarity : 0.005 0.086 1739 Dihedral : 5.896 53.669 1327 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.96 % Favored : 91.04 % Rotamer: Outliers : 5.37 % Allowed : 23.35 % Favored : 71.29 % 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: -0.79 (0.25), residues: 1206 helix: 0.00 (0.31), residues: 312 sheet: 0.72 (0.29), residues: 340 loop : -1.66 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 341 HIS 0.007 0.001 HIS Q 480 PHE 0.016 0.002 PHE Q 494 TYR 0.056 0.002 TYR Q 527 ARG 0.008 0.001 ARG Q 595 *********************** 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 218 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 158 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 89 MET cc_start: 0.6768 (mmt) cc_final: 0.6537 (mmt) REVERT: Q 283 ILE cc_start: 0.8905 (mm) cc_final: 0.8649 (mm) REVERT: Q 323 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6407 (mmt90) REVERT: Q 576 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: Q 660 PHE cc_start: 0.8088 (p90) cc_final: 0.7887 (p90) REVERT: Q 1024 SER cc_start: 0.9256 (t) cc_final: 0.9034 (t) REVERT: Q 1156 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 60 outliers final: 40 residues processed: 195 average time/residue: 0.2230 time to fit residues: 60.6785 Evaluate side-chains 191 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 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 326 ILE Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 492 LEU Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 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 1080 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 516 ASN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10191 Z= 0.175 Angle : 0.704 16.966 13809 Z= 0.343 Chirality : 0.045 0.204 1578 Planarity : 0.005 0.085 1739 Dihedral : 5.796 57.237 1327 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.13 % Favored : 91.87 % Rotamer: Outliers : 4.65 % Allowed : 25.31 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1206 helix: 0.10 (0.31), residues: 313 sheet: 0.91 (0.30), residues: 326 loop : -1.63 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Q 589 HIS 0.005 0.001 HIS Q 480 PHE 0.010 0.001 PHE Q1166 TYR 0.056 0.002 TYR Q 527 ARG 0.007 0.000 ARG Q1264 *********************** 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 205 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 153 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6849 (tm-30) REVERT: Q 181 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8659 (mt) REVERT: Q 283 ILE cc_start: 0.8896 (mm) cc_final: 0.8609 (mm) REVERT: Q 323 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.6373 (mmt90) REVERT: Q 775 LEU cc_start: 0.7788 (tt) cc_final: 0.7549 (tp) REVERT: Q 990 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8467 (mtmt) REVERT: Q 1024 SER cc_start: 0.9237 (t) cc_final: 0.9003 (t) REVERT: Q 1156 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8126 (tp) outliers start: 52 outliers final: 32 residues processed: 192 average time/residue: 0.2201 time to fit residues: 59.1797 Evaluate side-chains 181 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 148 LEU 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 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 326 ILE Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 447 TYR 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 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 951 VAL Chi-restraints excluded: chain Q residue 990 LYS 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 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 1360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 222 HIS ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10191 Z= 0.171 Angle : 0.696 15.309 13809 Z= 0.340 Chirality : 0.045 0.235 1578 Planarity : 0.005 0.084 1739 Dihedral : 5.739 58.830 1327 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.13 % Favored : 91.96 % Rotamer: Outliers : 4.38 % Allowed : 25.13 % Favored : 70.48 % 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: -0.68 (0.25), residues: 1206 helix: 0.08 (0.31), residues: 313 sheet: 0.89 (0.30), residues: 326 loop : -1.60 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Q 341 HIS 0.004 0.001 HIS Q 593 PHE 0.012 0.001 PHE Q1155 TYR 0.055 0.001 TYR Q 527 ARG 0.005 0.001 ARG Q1264 *********************** 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 203 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 154 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6806 (tm-30) REVERT: Q 85 TYR cc_start: 0.7277 (m-80) cc_final: 0.6896 (m-80) REVERT: Q 181 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8685 (mt) REVERT: Q 283 ILE cc_start: 0.8814 (mm) cc_final: 0.8553 (mm) REVERT: Q 323 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6424 (mmt90) REVERT: Q 368 MET cc_start: 0.8629 (tpp) cc_final: 0.8360 (tmm) REVERT: Q 484 MET cc_start: 0.5415 (mtm) cc_final: 0.5194 (mtm) REVERT: Q 566 LEU cc_start: 0.8361 (mt) cc_final: 0.7902 (mt) REVERT: Q 605 LEU cc_start: 0.6895 (pt) cc_final: 0.6315 (pp) REVERT: Q 775 LEU cc_start: 0.7825 (tt) cc_final: 0.7538 (tp) REVERT: Q 990 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8424 (mtmt) REVERT: Q 1024 SER cc_start: 0.9232 (t) cc_final: 0.9009 (t) REVERT: Q 1263 MET cc_start: 0.8696 (mmm) cc_final: 0.8433 (mtt) outliers start: 49 outliers final: 33 residues processed: 192 average time/residue: 0.2195 time to fit residues: 59.4647 Evaluate side-chains 181 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 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 411 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 539 VAL Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 599 HIS 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 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 46 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2933 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= 0.210 Angle : 0.714 14.057 13809 Z= 0.348 Chirality : 0.046 0.231 1578 Planarity : 0.005 0.082 1739 Dihedral : 5.492 47.696 1325 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.13 % Favored : 91.96 % Rotamer: Outliers : 4.47 % Allowed : 25.67 % Favored : 69.86 % 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: -0.73 (0.25), residues: 1206 helix: 0.10 (0.31), residues: 314 sheet: 0.86 (0.30), residues: 319 loop : -1.65 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 207 HIS 0.005 0.001 HIS Q 593 PHE 0.012 0.001 PHE Q1155 TYR 0.061 0.002 TYR Q 527 ARG 0.006 0.001 ARG Q 595 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6895 (tm-30) REVERT: Q 85 TYR cc_start: 0.7300 (m-80) cc_final: 0.6879 (m-80) REVERT: Q 181 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8644 (mt) REVERT: Q 283 ILE cc_start: 0.8877 (mm) cc_final: 0.8639 (mm) REVERT: Q 323 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.6435 (mmt90) REVERT: Q 678 TRP cc_start: 0.8345 (m100) cc_final: 0.8069 (m100) REVERT: Q 990 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8477 (mtmt) REVERT: Q 1024 SER cc_start: 0.9258 (t) cc_final: 0.9042 (t) REVERT: Q 1156 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8150 (tp) REVERT: Q 1263 MET cc_start: 0.8793 (mmm) cc_final: 0.8456 (mtt) outliers start: 50 outliers final: 34 residues processed: 197 average time/residue: 0.2150 time to fit residues: 59.8776 Evaluate side-chains 189 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 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 411 VAL Chi-restraints excluded: chain Q residue 425 ILE 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 539 VAL Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 599 HIS 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 1072 SER Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1156 LEU Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 516 ASN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10191 Z= 0.177 Angle : 0.716 13.253 13809 Z= 0.347 Chirality : 0.045 0.244 1578 Planarity : 0.005 0.085 1739 Dihedral : 5.432 47.876 1325 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.05 % Favored : 92.04 % Rotamer: Outliers : 3.67 % Allowed : 26.83 % Favored : 69.50 % 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: -0.67 (0.25), residues: 1206 helix: 0.14 (0.31), residues: 313 sheet: 0.90 (0.30), residues: 319 loop : -1.60 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Q 207 HIS 0.005 0.001 HIS Q 593 PHE 0.012 0.001 PHE Q1155 TYR 0.059 0.002 TYR Q 527 ARG 0.006 0.000 ARG Q 583 *********************** 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 202 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6878 (tm-30) REVERT: Q 85 TYR cc_start: 0.7248 (m-80) cc_final: 0.6777 (m-80) REVERT: Q 181 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8729 (mt) REVERT: Q 283 ILE cc_start: 0.8796 (mm) cc_final: 0.8578 (mm) REVERT: Q 323 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6467 (mmt90) REVERT: Q 329 GLU cc_start: 0.8063 (tt0) cc_final: 0.7035 (tt0) REVERT: Q 644 LEU cc_start: 0.8312 (tp) cc_final: 0.7967 (pt) REVERT: Q 990 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (mtmt) REVERT: Q 1024 SER cc_start: 0.9239 (t) cc_final: 0.9008 (t) REVERT: Q 1156 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8092 (tp) REVERT: Q 1263 MET cc_start: 0.8782 (mmm) cc_final: 0.8461 (mtt) REVERT: Q 1363 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8482 (mp0) outliers start: 41 outliers final: 33 residues processed: 191 average time/residue: 0.2219 time to fit residues: 59.2722 Evaluate side-chains 188 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain Q residue 199 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 326 ILE Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 425 ILE Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 539 VAL Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 599 HIS 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 1123 VAL Chi-restraints excluded: chain Q residue 1156 LEU 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 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10191 Z= 0.170 Angle : 0.740 18.137 13809 Z= 0.355 Chirality : 0.046 0.257 1578 Planarity : 0.005 0.088 1739 Dihedral : 5.381 47.018 1325 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.05 % Favored : 92.12 % Rotamer: Outliers : 3.76 % Allowed : 26.74 % Favored : 69.50 % 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: -0.63 (0.25), residues: 1206 helix: 0.10 (0.31), residues: 315 sheet: 0.95 (0.30), residues: 319 loop : -1.55 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP Q 207 HIS 0.007 0.001 HIS Q 593 PHE 0.011 0.001 PHE Q1155 TYR 0.061 0.001 TYR Q 527 ARG 0.004 0.000 ARG Q 583 ********************** 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 198 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6867 (tm-30) REVERT: Q 181 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8758 (mt) REVERT: Q 283 ILE cc_start: 0.8800 (mm) cc_final: 0.8588 (mm) REVERT: Q 323 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.6505 (mmt90) REVERT: Q 329 GLU cc_start: 0.8017 (tt0) cc_final: 0.7005 (tt0) REVERT: Q 332 ARG cc_start: 0.6044 (tpp80) cc_final: 0.5666 (tpp80) REVERT: Q 605 LEU cc_start: 0.6910 (pt) cc_final: 0.6381 (pp) REVERT: Q 644 LEU cc_start: 0.8305 (tp) cc_final: 0.7941 (pt) REVERT: Q 775 LEU cc_start: 0.7818 (tt) cc_final: 0.7614 (tp) REVERT: Q 990 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8431 (mtmt) REVERT: Q 1024 SER cc_start: 0.9226 (t) cc_final: 0.8977 (t) REVERT: Q 1156 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8115 (tp) REVERT: Q 1263 MET cc_start: 0.8703 (mmm) cc_final: 0.8436 (mtt) REVERT: Q 1363 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8394 (mp0) outliers start: 42 outliers final: 33 residues processed: 189 average time/residue: 0.2134 time to fit residues: 57.3371 Evaluate side-chains 186 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 199 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 319 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 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 539 VAL Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 599 HIS 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 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 1360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0070 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.111178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095656 restraints weight = 31130.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098247 restraints weight = 18439.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100025 restraints weight = 12721.802| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10191 Z= 0.168 Angle : 0.735 17.370 13809 Z= 0.353 Chirality : 0.046 0.263 1578 Planarity : 0.005 0.087 1739 Dihedral : 5.345 46.470 1325 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.46 % Favored : 91.71 % Rotamer: Outliers : 4.03 % Allowed : 26.21 % 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: -0.64 (0.25), residues: 1206 helix: 0.09 (0.31), residues: 316 sheet: 0.97 (0.30), residues: 319 loop : -1.58 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Q 207 HIS 0.007 0.001 HIS Q 593 PHE 0.011 0.001 PHE Q1155 TYR 0.062 0.002 TYR Q 527 ARG 0.004 0.000 ARG Q1264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.95 seconds wall clock time: 40 minutes 9.15 seconds (2409.15 seconds total)