Starting phenix.real_space_refine on Wed Feb 14 15:26:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwq_16294/02_2024/8bwq_16294_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwq_16294/02_2024/8bwq_16294.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/8bwq_16294/02_2024/8bwq_16294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwq_16294/02_2024/8bwq_16294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwq_16294/02_2024/8bwq_16294_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwq_16294/02_2024/8bwq_16294_updated.pdb" } 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 43 5.16 5 C 6224 2.51 5 N 1605 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9576 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'TTC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.54 Number of scatterers: 9576 At special positions: 0 Unit cell: (77.376, 108.16, 146.432, 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 43 16.00 O 1704 8.00 N 1605 7.00 C 6224 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: 3.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 4 sheets defined 66.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 18 through 21 No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 25 through 36 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 73 removed outlier: 4.301A pdb=" N LYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 121 removed outlier: 4.916A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 4.111A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 151 through 180 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 203 through 281 removed outlier: 4.009A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N HIS A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.817A pdb=" N ILE A 233 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY A 234 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 241 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.861A pdb=" N PHE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 270 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 272 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 276 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 292 through 341 removed outlier: 3.797A pdb=" N LEU A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.868A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 391 removed outlier: 3.522A pdb=" N GLU A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 537 through 551 removed outlier: 3.631A pdb=" N ARG A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 575 removed outlier: 4.688A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 580 No H-bonds generated for 'chain 'A' and resid 577 through 580' Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 711 through 744 removed outlier: 3.621A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 806 removed outlier: 3.929A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.957A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 836 through 860 Processing helix chain 'A' and resid 862 through 896 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 3.839A pdb=" N LEU A 883 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 890 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 919 through 969 removed outlier: 4.505A pdb=" N GLN A 924 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 932 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 939 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 942 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 944 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 950 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 953 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 955 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS A 956 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 965 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 966 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1017 removed outlier: 3.660A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 4.072A pdb=" N LEU A1084 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1110 through 1116 removed outlier: 4.228A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1135 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1154 through 1158 removed outlier: 3.972A pdb=" N GLU A1157 " --> pdb=" O GLN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1179 through 1193 Processing helix chain 'A' and resid 1203 through 1206 Processing helix chain 'A' and resid 1209 through 1222 Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 3.512A pdb=" N GLU A1286 " --> pdb=" O ALA A1283 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 436 Processing sheet with id= B, first strand: chain 'A' and resid 610 through 613 removed outlier: 6.976A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= D, first strand: chain 'A' and resid 1251 through 1256 removed outlier: 6.461A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY A1075 " --> pdb=" O THR A1230 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1221 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: 3.01 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1729 1.32 - 1.45: 2420 1.45 - 1.57: 5563 1.57 - 1.69: 2 1.69 - 1.81: 70 Bond restraints: 9784 Sorted by residual: bond pdb=" C14 TTC A1401 " pdb=" N12 TTC A1401 " ideal model delta sigma weight residual 1.375 1.479 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C11 TTC A1401 " pdb=" N12 TTC A1401 " ideal model delta sigma weight residual 1.463 1.533 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C13 TTC A1401 " pdb=" C9 TTC A1401 " ideal model delta sigma weight residual 1.456 1.523 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C14 TTC A1401 " pdb=" C15 TTC A1401 " ideal model delta sigma weight residual 1.441 1.508 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C20 TTC A1401 " pdb=" O22 TTC A1401 " ideal model delta sigma weight residual 1.320 1.381 -0.061 2.00e-02 2.50e+03 9.20e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.22: 147 105.22 - 112.93: 5512 112.93 - 120.64: 4537 120.64 - 128.35: 2984 128.35 - 136.06: 88 Bond angle restraints: 13268 Sorted by residual: angle pdb=" CA TYR A 985 " pdb=" CB TYR A 985 " pdb=" CG TYR A 985 " ideal model delta sigma weight residual 113.90 108.55 5.35 1.80e+00 3.09e-01 8.82e+00 angle pdb=" C LEU A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta sigma weight residual 122.31 116.79 5.52 2.00e+00 2.50e-01 7.62e+00 angle pdb=" N PHE A 205 " pdb=" CA PHE A 205 " pdb=" C PHE A 205 " ideal model delta sigma weight residual 112.38 115.65 -3.27 1.22e+00 6.72e-01 7.20e+00 angle pdb=" C CYS A 161 " pdb=" N ALA A 162 " pdb=" CA ALA A 162 " ideal model delta sigma weight residual 120.28 116.84 3.44 1.34e+00 5.57e-01 6.58e+00 angle pdb=" C LEU A 730 " pdb=" N GLN A 731 " pdb=" CA GLN A 731 " ideal model delta sigma weight residual 120.44 117.20 3.24 1.30e+00 5.92e-01 6.22e+00 ... (remaining 13263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5419 17.60 - 35.21: 340 35.21 - 52.81: 61 52.81 - 70.41: 10 70.41 - 88.02: 13 Dihedral angle restraints: 5843 sinusoidal: 2349 harmonic: 3494 Sorted by residual: dihedral pdb=" CA ASP A 834 " pdb=" C ASP A 834 " pdb=" N LEU A 835 " pdb=" CA LEU A 835 " ideal model delta harmonic sigma weight residual 180.00 -150.62 -29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG A 37 " pdb=" C ARG A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLN A1154 " pdb=" C GLN A1154 " pdb=" N LEU A1155 " pdb=" CA LEU A1155 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 915 0.041 - 0.081: 441 0.081 - 0.122: 138 0.122 - 0.163: 42 0.163 - 0.204: 2 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA HIS A 158 " pdb=" N HIS A 158 " pdb=" C HIS A 158 " pdb=" CB HIS A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE A 205 " pdb=" N PHE A 205 " pdb=" C PHE A 205 " pdb=" CB PHE A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA LYS A1102 " pdb=" N LYS A1102 " pdb=" C LYS A1102 " pdb=" CB LYS A1102 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1535 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A1401 " -0.016 2.00e-02 2.50e+03 2.61e-02 3.75e+01 pdb=" C11 TTC A1401 " 0.036 2.00e-02 2.50e+03 pdb=" C13 TTC A1401 " 0.041 2.00e-02 2.50e+03 pdb=" C14 TTC A1401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 TTC A1401 " -0.018 2.00e-02 2.50e+03 pdb=" C16 TTC A1401 " -0.002 2.00e-02 2.50e+03 pdb=" C17 TTC A1401 " 0.029 2.00e-02 2.50e+03 pdb=" C19 TTC A1401 " -0.054 2.00e-02 2.50e+03 pdb=" C2 TTC A1401 " -0.019 2.00e-02 2.50e+03 pdb=" C21 TTC A1401 " -0.010 2.00e-02 2.50e+03 pdb=" C27 TTC A1401 " -0.009 2.00e-02 2.50e+03 pdb=" C3 TTC A1401 " -0.018 2.00e-02 2.50e+03 pdb=" C4 TTC A1401 " -0.005 2.00e-02 2.50e+03 pdb=" C5 TTC A1401 " 0.004 2.00e-02 2.50e+03 pdb=" C6 TTC A1401 " 0.005 2.00e-02 2.50e+03 pdb=" C7 TTC A1401 " 0.016 2.00e-02 2.50e+03 pdb=" C8 TTC A1401 " 0.030 2.00e-02 2.50e+03 pdb=" C9 TTC A1401 " 0.046 2.00e-02 2.50e+03 pdb=" N10 TTC A1401 " 0.018 2.00e-02 2.50e+03 pdb=" N12 TTC A1401 " 0.014 2.00e-02 2.50e+03 pdb=" O18 TTC A1401 " -0.035 2.00e-02 2.50e+03 pdb=" O26 TTC A1401 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.002 2.00e-02 2.50e+03 1.90e-02 7.25e+00 pdb=" CG TYR A 917 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.003 2.00e-02 2.50e+03 1.80e-02 6.46e+00 pdb=" CG TYR A 157 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.026 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1961 2.77 - 3.30: 10688 3.30 - 3.84: 15932 3.84 - 4.37: 19496 4.37 - 4.90: 31460 Nonbonded interactions: 79537 Sorted by model distance: nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.238 2.440 nonbonded pdb=" ND1 HIS A 35 " pdb=" OE1 GLU A 884 " model vdw 2.246 2.520 nonbonded pdb=" O GLN A1068 " pdb=" NZ LYS A1070 " model vdw 2.265 2.520 nonbonded pdb=" O SER A 563 " pdb=" NE2 GLN A 593 " model vdw 2.362 2.520 nonbonded pdb=" NH1 ARG A1220 " pdb=" OD2 ASP A1240 " model vdw 2.365 2.520 ... (remaining 79532 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=0.00 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: 8.050 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: 0.000 Extract box with map and model: 13.810 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 9784 Z= 0.596 Angle : 0.890 8.171 13268 Z= 0.478 Chirality : 0.052 0.204 1538 Planarity : 0.008 0.087 1642 Dihedral : 13.092 88.017 3577 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1187 helix: -1.06 (0.16), residues: 770 sheet: -0.45 (0.50), residues: 72 loop : 0.16 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 89 HIS 0.007 0.002 HIS A 798 PHE 0.026 0.003 PHE A 418 TYR 0.030 0.006 TYR A 917 ARG 0.020 0.002 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8134 (mt) cc_final: 0.7857 (tt) REVERT: A 63 PHE cc_start: 0.8844 (m-80) cc_final: 0.8610 (m-10) REVERT: A 142 THR cc_start: 0.9443 (m) cc_final: 0.9205 (p) REVERT: A 241 MET cc_start: 0.8749 (mmm) cc_final: 0.8411 (mpp) REVERT: A 333 PHE cc_start: 0.8903 (t80) cc_final: 0.8355 (t80) REVERT: A 337 THR cc_start: 0.9118 (m) cc_final: 0.8832 (m) REVERT: A 388 THR cc_start: 0.9039 (m) cc_final: 0.8625 (m) REVERT: A 415 PHE cc_start: 0.8862 (t80) cc_final: 0.8562 (t80) REVERT: A 558 LEU cc_start: 0.8099 (mt) cc_final: 0.7780 (tt) REVERT: A 577 CYS cc_start: 0.7907 (t) cc_final: 0.7463 (t) REVERT: A 1025 TRP cc_start: 0.8416 (m-10) cc_final: 0.7852 (m-10) REVERT: A 1043 PHE cc_start: 0.8570 (m-80) cc_final: 0.8199 (m-80) REVERT: A 1048 PHE cc_start: 0.7964 (t80) cc_final: 0.7509 (t80) REVERT: A 1069 GLU cc_start: 0.7876 (tt0) cc_final: 0.7650 (tp30) REVERT: A 1112 ASP cc_start: 0.7089 (m-30) cc_final: 0.6567 (m-30) REVERT: A 1120 ILE cc_start: 0.9253 (mt) cc_final: 0.8989 (mm) REVERT: A 1131 MET cc_start: 0.8803 (mmm) cc_final: 0.8588 (mmm) REVERT: A 1191 ILE cc_start: 0.9088 (mt) cc_final: 0.8851 (mt) REVERT: A 1201 ASP cc_start: 0.7276 (t0) cc_final: 0.7055 (t70) REVERT: A 1230 THR cc_start: 0.9250 (m) cc_final: 0.8920 (p) REVERT: A 1241 SER cc_start: 0.8639 (m) cc_final: 0.8382 (p) REVERT: A 1251 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7563 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2322 time to fit residues: 73.8304 Evaluate side-chains 161 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 122 ASN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 703 ASN A 903 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9784 Z= 0.285 Angle : 0.666 7.219 13268 Z= 0.358 Chirality : 0.042 0.151 1538 Planarity : 0.005 0.042 1642 Dihedral : 8.495 71.874 1308 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.82 % Allowed : 8.54 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1187 helix: -0.14 (0.17), residues: 781 sheet: -0.39 (0.54), residues: 69 loop : 0.39 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 89 HIS 0.010 0.001 HIS A1141 PHE 0.024 0.002 PHE A 433 TYR 0.023 0.002 TYR A1016 ARG 0.011 0.001 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8132 (mt) cc_final: 0.7843 (tt) REVERT: A 100 LEU cc_start: 0.9349 (tp) cc_final: 0.8902 (tt) REVERT: A 142 THR cc_start: 0.9132 (m) cc_final: 0.8908 (m) REVERT: A 286 ILE cc_start: 0.9587 (mm) cc_final: 0.9379 (mm) REVERT: A 292 GLU cc_start: 0.8538 (mp0) cc_final: 0.7925 (mt-10) REVERT: A 418 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: A 550 TYR cc_start: 0.7842 (t80) cc_final: 0.7109 (t80) REVERT: A 558 LEU cc_start: 0.8213 (mt) cc_final: 0.7689 (tt) REVERT: A 990 MET cc_start: 0.8157 (tpp) cc_final: 0.7922 (tpp) REVERT: A 1025 TRP cc_start: 0.8338 (m-10) cc_final: 0.6917 (m-10) REVERT: A 1043 PHE cc_start: 0.8386 (m-80) cc_final: 0.8114 (m-80) REVERT: A 1048 PHE cc_start: 0.8100 (t80) cc_final: 0.7351 (t80) REVERT: A 1069 GLU cc_start: 0.7847 (tt0) cc_final: 0.7547 (tp30) REVERT: A 1112 ASP cc_start: 0.6901 (m-30) cc_final: 0.6626 (m-30) REVERT: A 1120 ILE cc_start: 0.9340 (mt) cc_final: 0.9120 (mm) REVERT: A 1141 HIS cc_start: 0.8393 (m-70) cc_final: 0.8151 (m90) REVERT: A 1235 LEU cc_start: 0.9149 (mp) cc_final: 0.8833 (tt) outliers start: 19 outliers final: 11 residues processed: 201 average time/residue: 0.2094 time to fit residues: 60.2116 Evaluate side-chains 173 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9784 Z= 0.252 Angle : 0.605 7.891 13268 Z= 0.320 Chirality : 0.040 0.160 1538 Planarity : 0.004 0.035 1642 Dihedral : 7.575 72.136 1308 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 11.13 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1187 helix: 0.04 (0.18), residues: 781 sheet: -0.19 (0.56), residues: 69 loop : 0.57 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 89 HIS 0.007 0.001 HIS A1141 PHE 0.018 0.002 PHE A 415 TYR 0.020 0.002 TYR A 499 ARG 0.006 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.043 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: A 13 LEU cc_start: 0.8151 (mt) cc_final: 0.7886 (tt) REVERT: A 39 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7501 (mm) REVERT: A 103 GLU cc_start: 0.7566 (pp20) cc_final: 0.7351 (pp20) REVERT: A 221 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: A 236 SER cc_start: 0.9098 (m) cc_final: 0.8893 (m) REVERT: A 550 TYR cc_start: 0.8096 (t80) cc_final: 0.7331 (t80) REVERT: A 558 LEU cc_start: 0.7997 (mt) cc_final: 0.7519 (tt) REVERT: A 605 ILE cc_start: 0.6919 (mm) cc_final: 0.6628 (mm) REVERT: A 912 TRP cc_start: 0.8354 (m-90) cc_final: 0.8062 (m100) REVERT: A 1043 PHE cc_start: 0.8362 (m-80) cc_final: 0.8030 (m-80) REVERT: A 1046 VAL cc_start: 0.9175 (t) cc_final: 0.8970 (m) REVERT: A 1069 GLU cc_start: 0.7761 (tt0) cc_final: 0.7489 (tp30) REVERT: A 1120 ILE cc_start: 0.9368 (mt) cc_final: 0.9161 (mm) REVERT: A 1201 ASP cc_start: 0.7346 (t70) cc_final: 0.7143 (t0) REVERT: A 1216 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8627 (mm110) REVERT: A 1259 TYR cc_start: 0.8461 (t80) cc_final: 0.7669 (t80) outliers start: 32 outliers final: 22 residues processed: 199 average time/residue: 0.1927 time to fit residues: 55.9548 Evaluate side-chains 183 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1244 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0770 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 0.0010 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 0.0000 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN A 731 GLN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9784 Z= 0.161 Angle : 0.581 8.474 13268 Z= 0.300 Chirality : 0.039 0.141 1538 Planarity : 0.004 0.036 1642 Dihedral : 6.603 62.342 1308 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.63 % Allowed : 14.88 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1187 helix: 0.35 (0.18), residues: 775 sheet: 0.23 (0.56), residues: 79 loop : 0.49 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 89 HIS 0.005 0.001 HIS A 153 PHE 0.019 0.001 PHE A1048 TYR 0.019 0.001 TYR A1259 ARG 0.006 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 SER cc_start: 0.9085 (m) cc_final: 0.8881 (m) REVERT: A 418 PHE cc_start: 0.7403 (m-80) cc_final: 0.7165 (m-80) REVERT: A 483 TRP cc_start: 0.7747 (t60) cc_final: 0.7337 (t60) REVERT: A 495 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: A 550 TYR cc_start: 0.8206 (t80) cc_final: 0.7377 (t80) REVERT: A 558 LEU cc_start: 0.7924 (mt) cc_final: 0.7581 (tt) REVERT: A 605 ILE cc_start: 0.6854 (mm) cc_final: 0.6625 (mm) REVERT: A 912 TRP cc_start: 0.8266 (m-90) cc_final: 0.7985 (m100) REVERT: A 1043 PHE cc_start: 0.8417 (m-80) cc_final: 0.8078 (m-80) REVERT: A 1048 PHE cc_start: 0.8107 (t80) cc_final: 0.7264 (t80) REVERT: A 1069 GLU cc_start: 0.7707 (tt0) cc_final: 0.7503 (tp30) REVERT: A 1120 ILE cc_start: 0.9400 (mt) cc_final: 0.9181 (mm) REVERT: A 1201 ASP cc_start: 0.7592 (t0) cc_final: 0.7372 (t70) REVERT: A 1216 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8610 (mm110) REVERT: A 1235 LEU cc_start: 0.9065 (mp) cc_final: 0.8712 (tt) outliers start: 17 outliers final: 11 residues processed: 203 average time/residue: 0.1974 time to fit residues: 58.3673 Evaluate side-chains 172 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 103 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9784 Z= 0.196 Angle : 0.587 8.649 13268 Z= 0.299 Chirality : 0.040 0.169 1538 Planarity : 0.004 0.034 1642 Dihedral : 6.148 56.288 1308 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.40 % Allowed : 15.93 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1187 helix: 0.38 (0.19), residues: 775 sheet: 0.44 (0.56), residues: 79 loop : 0.53 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 89 HIS 0.015 0.001 HIS A1111 PHE 0.015 0.001 PHE A1048 TYR 0.021 0.002 TYR A1259 ARG 0.008 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7053 (t70) cc_final: 0.6844 (t-90) REVERT: A 418 PHE cc_start: 0.7456 (m-80) cc_final: 0.7216 (m-80) REVERT: A 483 TRP cc_start: 0.7762 (t60) cc_final: 0.7241 (t60) REVERT: A 493 ILE cc_start: 0.9246 (mm) cc_final: 0.8641 (tp) REVERT: A 550 TYR cc_start: 0.8252 (t80) cc_final: 0.7331 (t80) REVERT: A 558 LEU cc_start: 0.7901 (mt) cc_final: 0.7580 (tt) REVERT: A 874 ILE cc_start: 0.9375 (mm) cc_final: 0.9158 (mt) REVERT: A 987 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 1048 PHE cc_start: 0.8143 (t80) cc_final: 0.7922 (t80) REVERT: A 1069 GLU cc_start: 0.7782 (tt0) cc_final: 0.7501 (tp30) REVERT: A 1120 ILE cc_start: 0.9360 (mt) cc_final: 0.9119 (mm) REVERT: A 1201 ASP cc_start: 0.7603 (t0) cc_final: 0.7202 (t0) REVERT: A 1216 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8646 (mm110) REVERT: A 1235 LEU cc_start: 0.9077 (mp) cc_final: 0.8807 (tt) outliers start: 25 outliers final: 19 residues processed: 191 average time/residue: 0.1906 time to fit residues: 53.1392 Evaluate side-chains 179 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9784 Z= 0.196 Angle : 0.580 8.698 13268 Z= 0.297 Chirality : 0.040 0.160 1538 Planarity : 0.004 0.033 1642 Dihedral : 5.954 49.268 1308 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 16.89 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1187 helix: 0.36 (0.19), residues: 780 sheet: 0.57 (0.58), residues: 79 loop : 0.52 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1025 HIS 0.009 0.001 HIS A1111 PHE 0.013 0.001 PHE A1048 TYR 0.023 0.001 TYR A1259 ARG 0.002 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.7422 (m-80) cc_final: 0.7203 (m-80) REVERT: A 493 ILE cc_start: 0.9231 (mm) cc_final: 0.8647 (tp) REVERT: A 550 TYR cc_start: 0.8267 (t80) cc_final: 0.7342 (t80) REVERT: A 558 LEU cc_start: 0.7839 (mt) cc_final: 0.7580 (tt) REVERT: A 887 ARG cc_start: 0.8065 (ptt90) cc_final: 0.7847 (ppt170) REVERT: A 987 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8970 (mt) REVERT: A 1043 PHE cc_start: 0.8172 (m-80) cc_final: 0.7957 (m-10) REVERT: A 1061 LEU cc_start: 0.8714 (tt) cc_final: 0.8453 (mm) REVERT: A 1069 GLU cc_start: 0.7856 (tt0) cc_final: 0.7563 (tp30) REVERT: A 1201 ASP cc_start: 0.7708 (t0) cc_final: 0.7253 (t0) REVERT: A 1216 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8656 (mm110) outliers start: 27 outliers final: 20 residues processed: 188 average time/residue: 0.1736 time to fit residues: 48.5908 Evaluate side-chains 176 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9784 Z= 0.188 Angle : 0.587 9.597 13268 Z= 0.298 Chirality : 0.040 0.179 1538 Planarity : 0.004 0.032 1642 Dihedral : 5.813 50.538 1308 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 18.23 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1187 helix: 0.36 (0.18), residues: 778 sheet: 0.46 (0.58), residues: 79 loop : 0.58 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 89 HIS 0.005 0.001 HIS A1111 PHE 0.013 0.001 PHE A 336 TYR 0.018 0.001 TYR A1270 ARG 0.002 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.7413 (m-80) cc_final: 0.7175 (m-80) REVERT: A 493 ILE cc_start: 0.9198 (mm) cc_final: 0.8639 (tp) REVERT: A 550 TYR cc_start: 0.8294 (t80) cc_final: 0.7377 (t80) REVERT: A 558 LEU cc_start: 0.7873 (mt) cc_final: 0.7619 (tt) REVERT: A 605 ILE cc_start: 0.7329 (mm) cc_final: 0.6960 (mm) REVERT: A 887 ARG cc_start: 0.8090 (ptt90) cc_final: 0.7889 (ppt170) REVERT: A 987 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8947 (mt) REVERT: A 1010 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9130 (p) REVERT: A 1043 PHE cc_start: 0.8164 (m-80) cc_final: 0.7958 (m-10) REVERT: A 1061 LEU cc_start: 0.8756 (tt) cc_final: 0.8478 (mm) REVERT: A 1069 GLU cc_start: 0.7792 (tt0) cc_final: 0.7534 (tp30) REVERT: A 1216 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8658 (mm110) REVERT: A 1269 PHE cc_start: 0.8538 (t80) cc_final: 0.8245 (t80) outliers start: 28 outliers final: 23 residues processed: 178 average time/residue: 0.1719 time to fit residues: 45.6040 Evaluate side-chains 181 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1244 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.185 Angle : 0.594 11.319 13268 Z= 0.298 Chirality : 0.040 0.154 1538 Planarity : 0.004 0.032 1642 Dihedral : 5.710 52.352 1308 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.59 % Allowed : 18.91 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1187 helix: 0.40 (0.19), residues: 778 sheet: 0.50 (0.59), residues: 79 loop : 0.57 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1025 HIS 0.004 0.001 HIS A1141 PHE 0.015 0.001 PHE A1177 TYR 0.015 0.001 TYR A1270 ARG 0.003 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.9147 (tt) cc_final: 0.8879 (tp) REVERT: A 409 MET cc_start: 0.4117 (pmm) cc_final: 0.3180 (mmt) REVERT: A 418 PHE cc_start: 0.7406 (m-80) cc_final: 0.7169 (m-80) REVERT: A 493 ILE cc_start: 0.9190 (mm) cc_final: 0.8651 (tp) REVERT: A 550 TYR cc_start: 0.8302 (t80) cc_final: 0.7390 (t80) REVERT: A 558 LEU cc_start: 0.7922 (mt) cc_final: 0.7685 (tt) REVERT: A 605 ILE cc_start: 0.7281 (mm) cc_final: 0.6925 (mm) REVERT: A 987 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8871 (mt) REVERT: A 1010 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9120 (p) REVERT: A 1061 LEU cc_start: 0.8805 (tt) cc_final: 0.8482 (mm) REVERT: A 1069 GLU cc_start: 0.7775 (tt0) cc_final: 0.7498 (tp30) REVERT: A 1147 TRP cc_start: 0.8466 (m100) cc_final: 0.7652 (m100) REVERT: A 1216 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8674 (mm110) REVERT: A 1244 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8160 (mp) outliers start: 27 outliers final: 24 residues processed: 179 average time/residue: 0.1763 time to fit residues: 47.3646 Evaluate side-chains 185 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1244 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.0050 chunk 68 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.178 Angle : 0.607 14.127 13268 Z= 0.302 Chirality : 0.040 0.178 1538 Planarity : 0.004 0.068 1642 Dihedral : 5.606 55.349 1308 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.50 % Allowed : 19.39 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1187 helix: 0.41 (0.19), residues: 782 sheet: 0.51 (0.59), residues: 79 loop : 0.53 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1025 HIS 0.006 0.001 HIS A 411 PHE 0.043 0.001 PHE A1269 TYR 0.012 0.001 TYR A1270 ARG 0.012 0.000 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.9126 (tt) cc_final: 0.8873 (tp) REVERT: A 288 MET cc_start: 0.8647 (mmm) cc_final: 0.8397 (mmm) REVERT: A 418 PHE cc_start: 0.7391 (m-80) cc_final: 0.7152 (m-80) REVERT: A 493 ILE cc_start: 0.9184 (mm) cc_final: 0.8647 (tp) REVERT: A 550 TYR cc_start: 0.8322 (t80) cc_final: 0.7429 (t80) REVERT: A 605 ILE cc_start: 0.7268 (mm) cc_final: 0.6910 (mm) REVERT: A 936 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 987 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8836 (mt) REVERT: A 1016 TYR cc_start: 0.7983 (m-10) cc_final: 0.7658 (m-80) REVERT: A 1069 GLU cc_start: 0.7762 (tt0) cc_final: 0.7486 (tp30) REVERT: A 1147 TRP cc_start: 0.8443 (m100) cc_final: 0.7620 (m100) REVERT: A 1216 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8672 (mm110) outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 0.1890 time to fit residues: 51.2855 Evaluate side-chains 177 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN A1274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9784 Z= 0.264 Angle : 0.661 14.681 13268 Z= 0.332 Chirality : 0.041 0.205 1538 Planarity : 0.004 0.032 1642 Dihedral : 5.634 56.278 1308 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.50 % Allowed : 19.96 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1187 helix: 0.31 (0.19), residues: 777 sheet: 0.73 (0.58), residues: 79 loop : 0.60 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1025 HIS 0.005 0.001 HIS A 798 PHE 0.042 0.002 PHE A1269 TYR 0.026 0.002 TYR A 289 ARG 0.003 0.000 ARG A1210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.9114 (tt) cc_final: 0.8853 (tp) REVERT: A 103 GLU cc_start: 0.7679 (pp20) cc_final: 0.7420 (pp20) REVERT: A 126 MET cc_start: 0.7750 (mpp) cc_final: 0.7430 (mmp) REVERT: A 288 MET cc_start: 0.8722 (mmm) cc_final: 0.8431 (mmm) REVERT: A 418 PHE cc_start: 0.7427 (m-80) cc_final: 0.7170 (m-80) REVERT: A 493 ILE cc_start: 0.9199 (mm) cc_final: 0.8670 (tp) REVERT: A 550 TYR cc_start: 0.8325 (t80) cc_final: 0.7446 (t80) REVERT: A 605 ILE cc_start: 0.7256 (mm) cc_final: 0.6927 (mm) REVERT: A 936 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 987 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8905 (mt) REVERT: A 1069 GLU cc_start: 0.7796 (tt0) cc_final: 0.7412 (tp30) REVERT: A 1147 TRP cc_start: 0.8463 (m100) cc_final: 0.7643 (m100) REVERT: A 1169 GLU cc_start: 0.7427 (mm-30) cc_final: 0.5900 (tp30) REVERT: A 1216 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8679 (mm110) outliers start: 26 outliers final: 25 residues processed: 171 average time/residue: 0.1739 time to fit residues: 44.7171 Evaluate side-chains 178 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1186 CYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1259 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 539 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.131223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095796 restraints weight = 22231.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099038 restraints weight = 11175.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101086 restraints weight = 7089.753| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9784 Z= 0.189 Angle : 0.642 14.547 13268 Z= 0.319 Chirality : 0.040 0.188 1538 Planarity : 0.004 0.033 1642 Dihedral : 5.637 59.548 1308 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.69 % Allowed : 20.25 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1187 helix: 0.40 (0.19), residues: 773 sheet: 0.77 (0.58), residues: 79 loop : 0.51 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1025 HIS 0.009 0.001 HIS A 411 PHE 0.043 0.001 PHE A1269 TYR 0.023 0.002 TYR A 289 ARG 0.002 0.000 ARG A1251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.75 seconds wall clock time: 42 minutes 45.36 seconds (2565.36 seconds total)