Starting phenix.real_space_refine on Thu Feb 15 06:53:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2024/7vgj_31971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2024/7vgj_31971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2024/7vgj_31971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2024/7vgj_31971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2024/7vgj_31971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2024/7vgj_31971_updated.pdb" } resolution = 3.98 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= 0.002 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 57 5.16 5 C 7413 2.51 5 N 1904 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "A GLU 788": "OE1" <-> "OE2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 882": "NH1" <-> "NH2" Residue "A ARG 930": "NH1" <-> "NH2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1164": "NH1" <-> "NH2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8753 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 27, 'TRANS': 1056} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2653 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 25, 'TRANS': 304} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Classifications: {'peptide': 1} Time building chain proxies: 6.52, per 1000 atoms: 0.57 Number of scatterers: 11460 At special positions: 0 Unit cell: (100.287, 107.378, 172.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 1 15.00 O 2085 8.00 N 1904 7.00 C 7413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 105 " distance=2.03 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: 5.12 Conformation dependent library (CDL) restraints added in 2.3 seconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 8 sheets defined 37.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.197A pdb=" N LYS A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.732A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N HIS A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 332 through 366 removed outlier: 3.554A pdb=" N LEU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.404A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 455 through 458 No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 511 through 518 removed outlier: 4.889A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.500A pdb=" N ILE A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 removed outlier: 4.089A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.520A pdb=" N PHE A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 842 through 845 No H-bonds generated for 'chain 'A' and resid 842 through 845' Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.537A pdb=" N CYS A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 removed outlier: 3.682A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 removed outlier: 4.030A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 896 through 899' Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 930 through 935 Processing helix chain 'A' and resid 940 through 972 removed outlier: 4.082A pdb=" N PHE A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 972 " --> pdb=" O TYR A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 991 No H-bonds generated for 'chain 'A' and resid 988 through 991' Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1032 through 1055 removed outlier: 3.768A pdb=" N LEU A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1043 " --> pdb=" O HIS A1039 " (cutoff:3.500A) Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1072 No H-bonds generated for 'chain 'A' and resid 1069 through 1072' Processing helix chain 'A' and resid 1074 through 1091 removed outlier: 4.244A pdb=" N ALA A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1118 removed outlier: 4.321A pdb=" N HIS A1118 " --> pdb=" O MET A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1123 No H-bonds generated for 'chain 'A' and resid 1120 through 1123' Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 5.325A pdb=" N ARG A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1170 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'B' and resid 50 through 61 removed outlier: 4.013A pdb=" N LEU B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 65 through 76 removed outlier: 4.038A pdb=" N THR B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.693A pdb=" N LEU B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 154' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 176 through 179 No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 258 through 264 Processing helix chain 'B' and resid 326 through 353 removed outlier: 3.599A pdb=" N VAL B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 224 through 226 Processing sheet with id= B, first strand: chain 'A' and resid 924 through 926 removed outlier: 6.308A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= D, first strand: chain 'A' and resid 576 through 581 removed outlier: 6.978A pdb=" N ILE A 606 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 593 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER A 604 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.700A pdb=" N LYS A 182 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG A 185 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.791A pdb=" N TYR A 658 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 700 " --> pdb=" O TYR A 658 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 105 through 113 removed outlier: 4.014A pdb=" N CYS B 105 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 293 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 191 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 185 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 312 through 317 removed outlier: 6.035A pdb=" N TYR B 125 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 275 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 127 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 273 " --> pdb=" O LEU B 127 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 963 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: 3.27 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1845 1.30 - 1.43: 3230 1.43 - 1.56: 6569 1.56 - 1.69: 2 1.69 - 1.81: 87 Bond restraints: 11733 Sorted by residual: bond pdb=" C17 P5S A1301 " pdb=" O19 P5S A1301 " ideal model delta sigma weight residual 1.328 1.401 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C38 P5S A1301 " pdb=" O37 P5S A1301 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N LEU A 294 " pdb=" CA LEU A 294 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.38e+00 bond pdb=" N HIS A 510 " pdb=" CA HIS A 510 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.28e-02 6.10e+03 6.53e+00 bond pdb=" N ASP A 454 " pdb=" CA ASP A 454 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.11e+00 ... (remaining 11728 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.09: 152 104.09 - 111.59: 5138 111.59 - 119.09: 4290 119.09 - 126.59: 6151 126.59 - 134.10: 159 Bond angle restraints: 15890 Sorted by residual: angle pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" CD PRO B 90 " ideal model delta sigma weight residual 112.00 105.18 6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" N PRO B 90 " pdb=" CD PRO B 90 " pdb=" CG PRO B 90 " ideal model delta sigma weight residual 103.20 96.59 6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" O13 P5S A1301 " pdb=" P12 P5S A1301 " pdb=" O15 P5S A1301 " ideal model delta sigma weight residual 120.39 107.76 12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N ASP A 289 " pdb=" CA ASP A 289 " pdb=" C ASP A 289 " ideal model delta sigma weight residual 108.19 113.31 -5.12 1.29e+00 6.01e-01 1.58e+01 angle pdb=" CA LEU A1125 " pdb=" CB LEU A1125 " pdb=" CG LEU A1125 " ideal model delta sigma weight residual 116.30 129.06 -12.76 3.50e+00 8.16e-02 1.33e+01 ... (remaining 15885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 6801 33.30 - 66.59: 155 66.59 - 99.89: 21 99.89 - 133.18: 0 133.18 - 166.48: 3 Dihedral angle restraints: 6980 sinusoidal: 2834 harmonic: 4146 Sorted by residual: dihedral pdb=" CA ILE B 171 " pdb=" C ILE B 171 " pdb=" N ALA B 172 " pdb=" CA ALA B 172 " ideal model delta harmonic sigma weight residual 180.00 -152.28 -27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA THR A 398 " pdb=" C THR A 398 " pdb=" N MET A 399 " pdb=" CA MET A 399 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU A 649 " pdb=" C GLU A 649 " pdb=" N THR A 650 " pdb=" CA THR A 650 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1215 0.048 - 0.097: 439 0.097 - 0.145: 90 0.145 - 0.194: 10 0.194 - 0.242: 5 Chirality restraints: 1759 Sorted by residual: chirality pdb=" CB ILE A 181 " pdb=" CA ILE A 181 " pdb=" CG1 ILE A 181 " pdb=" CG2 ILE A 181 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 394 " pdb=" CA ILE A 394 " pdb=" CG1 ILE A 394 " pdb=" CG2 ILE A 394 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLU B 161 " pdb=" N GLU B 161 " pdb=" C GLU B 161 " pdb=" CB GLU B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1756 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 133 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 134 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 89 " 0.045 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO B 90 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 302 " -0.012 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR B 302 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 302 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 302 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 302 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 302 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 302 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 302 " 0.001 2.00e-02 2.50e+03 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 732 2.71 - 3.26: 13102 3.26 - 3.80: 18791 3.80 - 4.35: 23372 4.35 - 4.90: 36994 Nonbonded interactions: 92991 Sorted by model distance: nonbonded pdb=" NZ LYS A 238 " pdb=" O PHE A 239 " model vdw 2.160 2.520 nonbonded pdb=" O PRO B 290 " pdb=" OH TYR B 294 " model vdw 2.168 2.440 nonbonded pdb=" NZ LYS A 240 " pdb=" O ILE A 293 " model vdw 2.197 2.520 nonbonded pdb=" NZ LYS B 235 " pdb=" O PRO B 236 " model vdw 2.203 2.520 nonbonded pdb=" O TYR A 992 " pdb=" OG SER A1106 " model vdw 2.205 2.440 ... (remaining 92986 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: 0.710 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: 3.590 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.007 0.079 11733 Z= 0.449 Angle : 0.911 12.761 15890 Z= 0.480 Chirality : 0.051 0.242 1759 Planarity : 0.005 0.070 2010 Dihedral : 15.687 166.477 4305 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.43 % Favored : 83.57 % Rotamer: Outliers : 0.48 % Allowed : 0.32 % Favored : 99.19 % 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: -3.55 (0.21), residues: 1406 helix: -1.32 (0.21), residues: 531 sheet: -2.05 (0.44), residues: 142 loop : -3.34 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 191 HIS 0.007 0.002 HIS A 535 PHE 0.019 0.002 PHE A 207 TYR 0.037 0.003 TYR B 302 ARG 0.012 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.352 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. REVERT: A 237 LEU cc_start: 0.8410 (tp) cc_final: 0.7599 (tp) REVERT: A 467 LYS cc_start: 0.8593 (tppt) cc_final: 0.8159 (tppp) REVERT: A 538 MET cc_start: 0.8515 (mpp) cc_final: 0.8051 (mpp) REVERT: A 875 MET cc_start: 0.8649 (tmm) cc_final: 0.8396 (tmm) REVERT: A 1113 ILE cc_start: 0.6186 (tp) cc_final: 0.5959 (tp) REVERT: B 163 TYR cc_start: 0.7418 (p90) cc_final: 0.6791 (p90) REVERT: B 314 ILE cc_start: 0.9068 (pt) cc_final: 0.8411 (pt) outliers start: 6 outliers final: 2 residues processed: 126 average time/residue: 0.1980 time to fit residues: 38.8889 Evaluate side-chains 104 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 692 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 67 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN A1061 GLN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11733 Z= 0.188 Angle : 0.678 10.316 15890 Z= 0.341 Chirality : 0.044 0.188 1759 Planarity : 0.004 0.046 2010 Dihedral : 9.866 158.694 1594 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 1.13 % Allowed : 9.98 % Favored : 88.89 % 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: -2.92 (0.22), residues: 1406 helix: -0.69 (0.22), residues: 537 sheet: -1.48 (0.46), residues: 142 loop : -3.14 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.007 0.001 HIS A 535 PHE 0.023 0.002 PHE A 853 TYR 0.024 0.002 TYR A 476 ARG 0.007 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.461 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. REVERT: A 467 LYS cc_start: 0.8930 (tppt) cc_final: 0.8590 (tptp) REVERT: A 538 MET cc_start: 0.8113 (mpp) cc_final: 0.7680 (mpp) REVERT: A 720 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8673 (mtmm) REVERT: A 992 TYR cc_start: 0.7965 (m-10) cc_final: 0.7336 (m-80) REVERT: B 163 TYR cc_start: 0.7427 (p90) cc_final: 0.6752 (p90) REVERT: B 313 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7779 (tmm) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.1882 time to fit residues: 41.4265 Evaluate side-chains 124 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11733 Z= 0.385 Angle : 0.735 9.701 15890 Z= 0.375 Chirality : 0.046 0.175 1759 Planarity : 0.004 0.041 2010 Dihedral : 9.971 164.911 1594 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 2.42 % Allowed : 15.62 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.22), residues: 1406 helix: -0.73 (0.22), residues: 532 sheet: -1.72 (0.45), residues: 146 loop : -3.16 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 191 HIS 0.007 0.002 HIS A 630 PHE 0.026 0.002 PHE B 217 TYR 0.022 0.002 TYR A 476 ARG 0.007 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.472 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. REVERT: A 467 LYS cc_start: 0.9031 (tppt) cc_final: 0.8751 (tppp) REVERT: A 538 MET cc_start: 0.8134 (mpp) cc_final: 0.7727 (mpp) REVERT: A 811 LEU cc_start: 0.8103 (tp) cc_final: 0.7895 (tp) REVERT: A 1142 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 163 TYR cc_start: 0.7804 (p90) cc_final: 0.6990 (p90) outliers start: 30 outliers final: 21 residues processed: 130 average time/residue: 0.1839 time to fit residues: 38.4782 Evaluate side-chains 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 122 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11733 Z= 0.183 Angle : 0.634 9.309 15890 Z= 0.319 Chirality : 0.042 0.161 1759 Planarity : 0.004 0.041 2010 Dihedral : 9.228 157.615 1594 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 2.17 % Allowed : 18.44 % Favored : 79.39 % 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: -2.67 (0.22), residues: 1406 helix: -0.44 (0.22), residues: 542 sheet: -1.23 (0.47), residues: 136 loop : -3.07 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.006 0.001 HIS A 535 PHE 0.020 0.001 PHE B 217 TYR 0.033 0.002 TYR A 476 ARG 0.006 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: A 538 MET cc_start: 0.8000 (mpp) cc_final: 0.7579 (mpp) REVERT: A 603 MET cc_start: 0.5709 (tmm) cc_final: 0.5461 (tmm) REVERT: A 811 LEU cc_start: 0.7965 (tp) cc_final: 0.7721 (tp) REVERT: A 992 TYR cc_start: 0.7911 (m-10) cc_final: 0.7295 (m-80) REVERT: B 40 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7789 (ptt90) REVERT: B 56 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 163 TYR cc_start: 0.7974 (p90) cc_final: 0.7152 (p90) outliers start: 27 outliers final: 16 residues processed: 141 average time/residue: 0.1951 time to fit residues: 43.8646 Evaluate side-chains 133 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 116 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 0.0370 chunk 122 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 545 GLN ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11733 Z= 0.218 Angle : 0.642 10.857 15890 Z= 0.321 Chirality : 0.042 0.153 1759 Planarity : 0.004 0.039 2010 Dihedral : 8.913 142.114 1591 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 3.06 % Allowed : 20.05 % Favored : 76.89 % 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: -2.56 (0.22), residues: 1406 helix: -0.35 (0.22), residues: 542 sheet: -1.30 (0.45), residues: 143 loop : -2.98 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.005 0.001 HIS A 535 PHE 0.021 0.001 PHE B 217 TYR 0.034 0.002 TYR A 476 ARG 0.005 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: A 538 MET cc_start: 0.7953 (mpp) cc_final: 0.7480 (mpp) REVERT: A 811 LEU cc_start: 0.7984 (tp) cc_final: 0.7764 (tp) REVERT: A 992 TYR cc_start: 0.7973 (m-10) cc_final: 0.7333 (m-80) REVERT: B 40 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7799 (ptt90) REVERT: B 56 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 163 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7231 (p90) outliers start: 38 outliers final: 25 residues processed: 143 average time/residue: 0.1882 time to fit residues: 42.5186 Evaluate side-chains 139 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 0.0060 chunk 131 optimal weight: 0.0770 overall best weight: 1.0156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 965 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11733 Z= 0.152 Angle : 0.624 11.024 15890 Z= 0.307 Chirality : 0.041 0.153 1759 Planarity : 0.004 0.041 2010 Dihedral : 8.233 122.330 1589 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 2.82 % Allowed : 21.18 % Favored : 76.01 % 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: -2.22 (0.23), residues: 1406 helix: -0.01 (0.23), residues: 525 sheet: -1.11 (0.45), residues: 142 loop : -2.78 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 191 HIS 0.005 0.001 HIS A 535 PHE 0.016 0.001 PHE B 217 TYR 0.031 0.001 TYR A 476 ARG 0.004 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8740 (tt) cc_final: 0.8380 (tt) REVERT: A 232 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6562 (p0) REVERT: A 538 MET cc_start: 0.7919 (mpp) cc_final: 0.7437 (mpp) REVERT: A 811 LEU cc_start: 0.7988 (tp) cc_final: 0.7746 (tp) REVERT: A 992 TYR cc_start: 0.7938 (m-10) cc_final: 0.7313 (m-80) REVERT: B 56 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7728 (mp) REVERT: B 58 PHE cc_start: 0.6956 (m-80) cc_final: 0.6294 (m-80) REVERT: B 163 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7186 (p90) REVERT: B 183 ASN cc_start: 0.5378 (OUTLIER) cc_final: 0.5152 (p0) outliers start: 35 outliers final: 19 residues processed: 168 average time/residue: 0.1977 time to fit residues: 51.5683 Evaluate side-chains 146 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11733 Z= 0.207 Angle : 0.658 13.055 15890 Z= 0.323 Chirality : 0.042 0.149 1759 Planarity : 0.004 0.081 2010 Dihedral : 8.180 114.631 1589 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 2.58 % Allowed : 23.75 % Favored : 73.67 % 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: -2.19 (0.23), residues: 1406 helix: -0.08 (0.23), residues: 529 sheet: -1.10 (0.44), residues: 155 loop : -2.70 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 191 HIS 0.004 0.001 HIS A 510 PHE 0.027 0.001 PHE A 529 TYR 0.027 0.002 TYR A 476 ARG 0.004 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.432 Fit side-chains REVERT: A 130 LEU cc_start: 0.8781 (tt) cc_final: 0.8383 (tt) REVERT: A 232 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6441 (p0) REVERT: A 538 MET cc_start: 0.7858 (mpp) cc_final: 0.7399 (mpp) REVERT: A 811 LEU cc_start: 0.7982 (tp) cc_final: 0.7752 (tp) REVERT: A 875 MET cc_start: 0.8664 (ppp) cc_final: 0.8450 (ppp) REVERT: A 992 TYR cc_start: 0.7937 (m-10) cc_final: 0.7255 (m-80) REVERT: B 56 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 58 PHE cc_start: 0.7024 (m-80) cc_final: 0.6286 (m-80) REVERT: B 163 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7235 (p90) outliers start: 32 outliers final: 22 residues processed: 153 average time/residue: 0.1963 time to fit residues: 47.1497 Evaluate side-chains 150 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.0170 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 0.0040 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 106 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 257 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11733 Z= 0.146 Angle : 0.642 16.151 15890 Z= 0.309 Chirality : 0.041 0.252 1759 Planarity : 0.004 0.043 2010 Dihedral : 7.576 99.061 1589 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.33 % Allowed : 24.72 % Favored : 72.95 % 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: -2.06 (0.23), residues: 1406 helix: 0.11 (0.23), residues: 524 sheet: -1.33 (0.40), residues: 178 loop : -2.63 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS A 535 PHE 0.016 0.001 PHE B 217 TYR 0.030 0.001 TYR A 476 ARG 0.009 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.364 Fit side-chains REVERT: A 130 LEU cc_start: 0.8615 (tt) cc_final: 0.8310 (tt) REVERT: A 232 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6565 (p0) REVERT: A 466 PHE cc_start: 0.7079 (t80) cc_final: 0.6569 (t80) REVERT: A 538 MET cc_start: 0.7884 (mpp) cc_final: 0.7403 (mpp) REVERT: A 603 MET cc_start: 0.4928 (tmm) cc_final: 0.4509 (tmm) REVERT: A 875 MET cc_start: 0.8619 (ppp) cc_final: 0.8394 (ppp) REVERT: A 992 TYR cc_start: 0.7856 (m-10) cc_final: 0.7245 (m-80) REVERT: B 56 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 163 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7078 (p90) REVERT: B 228 GLU cc_start: 0.7482 (pm20) cc_final: 0.7270 (pm20) outliers start: 29 outliers final: 20 residues processed: 159 average time/residue: 0.1831 time to fit residues: 45.2593 Evaluate side-chains 152 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11733 Z= 0.336 Angle : 0.717 13.720 15890 Z= 0.353 Chirality : 0.044 0.155 1759 Planarity : 0.004 0.038 2010 Dihedral : 8.168 119.678 1589 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 2.98 % Allowed : 24.32 % Favored : 72.71 % 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: -2.24 (0.23), residues: 1406 helix: -0.08 (0.23), residues: 528 sheet: -1.13 (0.43), residues: 162 loop : -2.77 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 191 HIS 0.006 0.001 HIS A 510 PHE 0.023 0.002 PHE B 217 TYR 0.026 0.002 TYR A 476 ARG 0.004 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.665 Fit side-chains REVERT: A 232 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6401 (p0) REVERT: A 538 MET cc_start: 0.7916 (mpp) cc_final: 0.7424 (mpp) REVERT: A 603 MET cc_start: 0.5263 (tmm) cc_final: 0.4921 (tmm) REVERT: A 811 LEU cc_start: 0.7998 (tp) cc_final: 0.7762 (tp) REVERT: A 875 MET cc_start: 0.8663 (ppp) cc_final: 0.8352 (ppp) REVERT: A 992 TYR cc_start: 0.7914 (m-10) cc_final: 0.7365 (m-80) REVERT: B 56 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7718 (mp) REVERT: B 163 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7305 (p90) REVERT: B 181 MET cc_start: 0.7885 (ttt) cc_final: 0.6959 (ttt) REVERT: B 297 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6770 (t0) outliers start: 37 outliers final: 29 residues processed: 151 average time/residue: 0.2053 time to fit residues: 49.1215 Evaluate side-chains 151 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.0270 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11733 Z= 0.151 Angle : 0.680 16.009 15890 Z= 0.323 Chirality : 0.042 0.190 1759 Planarity : 0.004 0.038 2010 Dihedral : 7.684 99.705 1589 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 2.17 % Allowed : 25.12 % Favored : 72.71 % 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: -2.07 (0.23), residues: 1406 helix: 0.07 (0.23), residues: 523 sheet: -1.13 (0.43), residues: 169 loop : -2.66 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 805 HIS 0.004 0.001 HIS A 535 PHE 0.023 0.001 PHE A 124 TYR 0.024 0.001 TYR A 476 ARG 0.004 0.000 ARG B 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6431 (p0) REVERT: A 538 MET cc_start: 0.7869 (mpp) cc_final: 0.6912 (tpt) REVERT: A 603 MET cc_start: 0.5024 (tmm) cc_final: 0.4659 (tmm) REVERT: A 875 MET cc_start: 0.8604 (ppp) cc_final: 0.8287 (ppp) REVERT: A 992 TYR cc_start: 0.7782 (m-10) cc_final: 0.7247 (m-80) REVERT: B 56 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7740 (mp) REVERT: B 163 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6982 (p90) REVERT: B 304 VAL cc_start: 0.8395 (m) cc_final: 0.8151 (p) outliers start: 27 outliers final: 21 residues processed: 152 average time/residue: 0.1884 time to fit residues: 44.7682 Evaluate side-chains 153 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.097573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073201 restraints weight = 40938.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.073894 restraints weight = 28608.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074011 restraints weight = 23165.445| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11733 Z= 0.190 Angle : 0.674 14.942 15890 Z= 0.320 Chirality : 0.042 0.178 1759 Planarity : 0.004 0.037 2010 Dihedral : 7.580 96.544 1589 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.25 % Allowed : 25.28 % Favored : 72.46 % 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: -1.97 (0.23), residues: 1406 helix: 0.17 (0.23), residues: 517 sheet: -1.01 (0.43), residues: 164 loop : -2.60 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS A 535 PHE 0.024 0.001 PHE B 340 TYR 0.023 0.002 TYR A 476 ARG 0.004 0.000 ARG B 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.84 seconds wall clock time: 40 minutes 12.39 seconds (2412.39 seconds total)