Starting phenix.real_space_refine (version: dev) on Mon Feb 20 05:16:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2023/7vgj_31971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2023/7vgj_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_2023/7vgj_31971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2023/7vgj_31971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2023/7vgj_31971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgj_31971/02_2023/7vgj_31971_updated.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 6.76, per 1000 atoms: 0.59 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: 4.85 Conformation dependent library (CDL) restraints added in 1.8 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: 1.84 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: 3.38 Time building geometry restraints manager: 5.18 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 - 31.95: 6767 31.95 - 63.90: 177 63.90 - 95.85: 22 95.85 - 127.81: 0 127.81 - 159.76: 2 Dihedral angle restraints: 6968 sinusoidal: 2822 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 6965 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 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. 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: 0.760 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: 3.940 Check model and map are aligned: 0.160 Process input model: 32.270 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 15.317 159.757 4293 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 % 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 *********************** 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 : 1.340 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 2 residues processed: 126 average time/residue: 0.1996 time to fit residues: 38.9802 Evaluate side-chains 101 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.447 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1127 time to fit residues: 2.2124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 67 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 145 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: 0.7734 moved from start: 0.1227 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= 0.175 Angle : 0.682 11.112 15890 Z= 0.340 Chirality : 0.044 0.186 1759 Planarity : 0.004 0.045 2010 Dihedral : 8.809 154.888 1577 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer Outliers : 0.97 % 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: -2.90 (0.22), residues: 1406 helix: -0.65 (0.22), residues: 543 sheet: -1.46 (0.46), residues: 142 loop : -3.17 (0.22), residues: 721 *********************** 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 147 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.406 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 6 residues processed: 140 average time/residue: 0.1979 time to fit residues: 43.5279 Evaluate side-chains 115 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.418 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1190 time to fit residues: 3.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.0170 chunk 39 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 114 optimal weight: 0.0170 chunk 127 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 overall best weight: 1.3460 ------------------------------------------------------------------------------- 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 899 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: 0.7728 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11733 Z= 0.168 Angle : 0.629 9.346 15890 Z= 0.315 Chirality : 0.042 0.158 1759 Planarity : 0.004 0.041 2010 Dihedral : 8.212 140.495 1577 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer Outliers : 1.21 % 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: -2.53 (0.22), residues: 1406 helix: -0.34 (0.23), residues: 535 sheet: -1.44 (0.45), residues: 145 loop : -2.89 (0.22), residues: 726 *********************** 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 144 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.272 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 0.2004 time to fit residues: 43.0645 Evaluate side-chains 126 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.465 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1288 time to fit residues: 3.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 67 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN ** 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 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11733 Z= 0.228 Angle : 0.652 9.122 15890 Z= 0.325 Chirality : 0.043 0.146 1759 Planarity : 0.004 0.037 2010 Dihedral : 8.079 135.319 1577 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer Outliers : 1.77 % 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: -2.54 (0.22), residues: 1406 helix: -0.38 (0.23), residues: 540 sheet: -1.41 (0.45), residues: 145 loop : -2.89 (0.22), residues: 721 *********************** 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 145 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.488 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 11 residues processed: 139 average time/residue: 0.1875 time to fit residues: 41.6572 Evaluate side-chains 130 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.307 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1130 time to fit residues: 4.3491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 1 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- 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 545 GLN A 917 GLN ** A 965 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7755 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 11733 Z= 0.205 Angle : 0.648 11.066 15890 Z= 0.321 Chirality : 0.042 0.152 1759 Planarity : 0.004 0.072 2010 Dihedral : 7.899 128.912 1577 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer Outliers : 1.77 % 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: -2.34 (0.23), residues: 1406 helix: -0.22 (0.23), residues: 529 sheet: -1.43 (0.44), residues: 150 loop : -2.70 (0.23), residues: 727 *********************** 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 153 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.357 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 8 residues processed: 145 average time/residue: 0.1815 time to fit residues: 41.9524 Evaluate side-chains 129 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.319 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1109 time to fit residues: 3.3431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.0060 chunk 136 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- 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 965 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11733 Z= 0.198 Angle : 0.663 12.627 15890 Z= 0.322 Chirality : 0.042 0.153 1759 Planarity : 0.004 0.039 2010 Dihedral : 7.767 123.327 1577 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 1.61 % 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: -0.16 (0.23), residues: 527 sheet: -1.11 (0.46), residues: 140 loop : -2.64 (0.23), residues: 739 *********************** 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 149 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.288 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 11 residues processed: 143 average time/residue: 0.1941 time to fit residues: 44.2786 Evaluate side-chains 133 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.400 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1069 time to fit residues: 4.0321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 76 optimal weight: 0.0670 chunk 135 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** 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: 0.7707 moved from start: 0.2450 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= 0.155 Angle : 0.649 15.333 15890 Z= 0.310 Chirality : 0.041 0.161 1759 Planarity : 0.003 0.038 2010 Dihedral : 7.419 110.702 1577 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.97 % 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: -2.08 (0.23), residues: 1406 helix: 0.01 (0.24), residues: 523 sheet: -1.12 (0.42), residues: 163 loop : -2.61 (0.23), residues: 720 *********************** 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 147 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.533 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 0.1964 time to fit residues: 44.6420 Evaluate side-chains 132 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.595 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1141 time to fit residues: 3.2576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2466 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= 0.194 Angle : 0.672 14.264 15890 Z= 0.323 Chirality : 0.042 0.147 1759 Planarity : 0.003 0.036 2010 Dihedral : 7.358 104.064 1577 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer Outliers : 0.97 % 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: 0.04 (0.23), residues: 526 sheet: -1.10 (0.42), residues: 164 loop : -2.62 (0.23), residues: 716 *********************** 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 139 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.400 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 9 residues processed: 133 average time/residue: 0.1949 time to fit residues: 41.3902 Evaluate side-chains 133 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.395 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1190 time to fit residues: 3.8274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.0970 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.2980 overall best weight: 2.0782 ------------------------------------------------------------------------------- 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** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11733 Z= 0.191 Angle : 0.673 14.366 15890 Z= 0.323 Chirality : 0.042 0.151 1759 Planarity : 0.003 0.036 2010 Dihedral : 7.279 100.153 1577 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer Outliers : 0.24 % 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: -2.03 (0.23), residues: 1406 helix: 0.09 (0.23), residues: 525 sheet: -1.07 (0.42), residues: 167 loop : -2.63 (0.23), residues: 714 *********************** 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 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.408 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 2 residues processed: 128 average time/residue: 0.2086 time to fit residues: 42.4296 Evaluate side-chains 127 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.264 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1323 time to fit residues: 2.1493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 111 optimal weight: 0.3980 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** ** 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: 0.7723 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11733 Z= 0.178 Angle : 0.675 14.550 15890 Z= 0.322 Chirality : 0.042 0.152 1759 Planarity : 0.003 0.036 2010 Dihedral : 7.182 98.433 1577 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 0.32 % 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: -1.96 (0.23), residues: 1406 helix: 0.10 (0.23), residues: 528 sheet: -1.05 (0.42), residues: 167 loop : -2.54 (0.24), residues: 711 ********************** 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 129 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.563 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 3 residues processed: 127 average time/residue: 0.1992 time to fit residues: 40.1692 Evaluate side-chains 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.461 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1236 time to fit residues: 2.8274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 0.0020 chunk 20 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 1.6090 ------------------------------------------------------------------------------- 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 545 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.098384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075145 restraints weight = 40520.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074305 restraints weight = 25217.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074382 restraints weight = 22237.210| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11733 Z= 0.169 Angle : 0.662 14.653 15890 Z= 0.316 Chirality : 0.041 0.158 1759 Planarity : 0.003 0.036 2010 Dihedral : 7.080 96.016 1577 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 0.48 % 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: 0.07 (0.23), residues: 539 sheet: -1.02 (0.42), residues: 167 loop : -2.59 (0.24), residues: 700 =============================================================================== Job complete usr+sys time: 1996.74 seconds wall clock time: 38 minutes 4.18 seconds (2284.18 seconds total)