Starting phenix.real_space_refine on Sun May 3 11:51:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fn4_4282/05_2026/6fn4_4282.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fn4_4282/05_2026/6fn4_4282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fn4_4282/05_2026/6fn4_4282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fn4_4282/05_2026/6fn4_4282.map" model { file = "/net/cci-nas-00/data/ceres_data/6fn4_4282/05_2026/6fn4_4282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fn4_4282/05_2026/6fn4_4282.cif" } resolution = 4.14 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 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= 0.015 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 48 5.16 5 C 8145 2.51 5 N 2122 2.21 5 O 2386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12702 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9182 Classifications: {'peptide': 1181} Link IDs: {'CIS': 5, 'PTRANS': 27, 'TRANS': 1148} Chain breaks: 1 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 207} Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'3PE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.98, per 1000 atoms: 0.23 Number of scatterers: 12702 At special positions: 0 Unit cell: (97.09, 98.477, 208.05, 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 48 16.00 P 1 15.00 O 2386 8.00 N 2122 7.00 C 8145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A1203 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM12649 O5 NAG A1303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1303 " - " ASN A 98 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 592.5 milliseconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 50.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.786A pdb=" N PHE A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 62 Processing helix chain 'A' and resid 64 through 88 removed outlier: 3.581A pdb=" N MET A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.343A pdb=" N ASP A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 156 removed outlier: 4.208A pdb=" N TYR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 166 through 186 removed outlier: 3.685A pdb=" N THR A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 208 removed outlier: 3.532A pdb=" N MET A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 removed outlier: 4.014A pdb=" N LEU A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Proline residue: A 222 - end of helix removed outlier: 4.421A pdb=" N SER A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 259 through 265 removed outlier: 3.773A pdb=" N ALA A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 321 Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.926A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 369 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.855A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.632A pdb=" N ILE A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.824A pdb=" N THR A 521 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 3.940A pdb=" N ARG A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 577 removed outlier: 4.007A pdb=" N ALA A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 619 through 629 removed outlier: 3.528A pdb=" N LYS A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 706 through 720 removed outlier: 4.031A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 738 removed outlier: 3.614A pdb=" N SER A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 798 Processing helix chain 'A' and resid 800 through 804 removed outlier: 3.552A pdb=" N ASP A 804 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 830 removed outlier: 4.508A pdb=" N GLY A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 828 " --> pdb=" O VAL A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 853 removed outlier: 3.710A pdb=" N VAL A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.740A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 880 removed outlier: 3.714A pdb=" N ILE A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 901 removed outlier: 4.033A pdb=" N LYS A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 909 removed outlier: 3.701A pdb=" N VAL A 906 " --> pdb=" O ASN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 963 removed outlier: 3.999A pdb=" N GLN A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 923 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 3.815A pdb=" N ALA A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 969 through 991 Processing helix chain 'A' and resid 997 through 1013 Processing helix chain 'A' and resid 1074 through 1083 removed outlier: 3.965A pdb=" N VAL A1078 " --> pdb=" O GLY A1074 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1126 through 1132 Processing helix chain 'A' and resid 1140 through 1151 removed outlier: 3.709A pdb=" N ILE A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A1145 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1159 removed outlier: 3.797A pdb=" N SER A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 4.144A pdb=" N ARG A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.897A pdb=" N VAL A1212 " --> pdb=" O GLU A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 3.898A pdb=" N ILE A1236 " --> pdb=" O ARG A1232 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1232 through 1237' Processing helix chain 'A' and resid 1255 through 1263 removed outlier: 3.627A pdb=" N LYS A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1273 removed outlier: 3.664A pdb=" N VAL A1272 " --> pdb=" O SER A1268 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN A1273 " --> pdb=" O MET A1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 189 through 195 removed outlier: 4.029A pdb=" N GLU B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 195' Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.945A pdb=" N ASP C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 91 " --> pdb=" O PHE C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 416 removed outlier: 6.547A pdb=" N LYS A 410 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS A 397 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU A 412 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 396 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP A 447 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 472 removed outlier: 6.292A pdb=" N GLY A 470 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASP A 554 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 472 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 551 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE A 584 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 553 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 607 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1059 removed outlier: 6.656A pdb=" N GLN A1053 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A1040 " --> pdb=" O GLN A1053 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A1055 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A1039 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A1090 " --> pdb=" O VAL A1039 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1113 through 1115 removed outlier: 6.116A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE A1229 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A1198 " --> pdb=" O ILE A1229 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A1065 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR A1064 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A1243 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA A1066 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A1245 " --> pdb=" O ALA A1066 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A1068 " --> pdb=" O ILE A1245 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A1242 " --> pdb=" O HIS A1253 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS A1253 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1244 " --> pdb=" O LYS A1251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1124 through 1125 Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.979A pdb=" N LEU B 11 " --> pdb=" O ASP B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 54 removed outlier: 5.256A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 124 removed outlier: 5.665A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 156 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.441A pdb=" N GLU C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N SER C 121 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 12 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.594A pdb=" N SER C 189 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 133 Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 163 716 hydrogen bonds defined for protein. 2028 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: 2.46 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2062 1.29 - 1.43: 3355 1.43 - 1.57: 7460 1.57 - 1.71: 2 1.71 - 1.84: 83 Bond restraints: 12962 Sorted by residual: bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.491 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.470 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.346 1.469 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 12957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 17485 4.50 - 9.01: 54 9.01 - 13.51: 7 13.51 - 18.02: 0 18.02 - 22.52: 1 Bond angle restraints: 17547 Sorted by residual: angle pdb=" O12 3PE A1304 " pdb=" P 3PE A1304 " pdb=" O14 3PE A1304 " ideal model delta sigma weight residual 123.79 101.27 22.52 3.00e+00 1.11e-01 5.64e+01 angle pdb=" C ASP A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta sigma weight residual 121.70 133.19 -11.49 1.80e+00 3.09e-01 4.07e+01 angle pdb=" C SER A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta sigma weight residual 121.70 131.52 -9.82 1.80e+00 3.09e-01 2.98e+01 angle pdb=" C VAL A 33 " pdb=" N SER A 34 " pdb=" CA SER A 34 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.98e+01 angle pdb=" C3 NAG A1302 " pdb=" C2 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 110.74 98.23 12.51 3.00e+00 1.11e-01 1.74e+01 ... (remaining 17542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 7365 16.25 - 32.50: 318 32.50 - 48.75: 69 48.75 - 65.00: 7 65.00 - 81.25: 7 Dihedral angle restraints: 7766 sinusoidal: 3089 harmonic: 4677 Sorted by residual: dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A1203 " pdb=" CB CYS A1203 " ideal model delta sinusoidal sigma weight residual -86.00 -159.27 73.27 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA ARG A 488 " pdb=" C ARG A 488 " pdb=" N TYR A 489 " pdb=" CA TYR A 489 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLY C 153 " pdb=" C GLY C 153 " pdb=" N TYR C 154 " pdb=" CA TYR C 154 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1362 0.041 - 0.083: 476 0.083 - 0.124: 142 0.124 - 0.166: 27 0.166 - 0.207: 1 Chirality restraints: 2008 Sorted by residual: chirality pdb=" CB ILE A 97 " pdb=" CA ILE A 97 " pdb=" CG1 ILE A 97 " pdb=" CG2 ILE A 97 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 839 " pdb=" CA ILE A 839 " pdb=" CG1 ILE A 839 " pdb=" CG2 ILE A 839 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 2005 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.062 2.00e-02 2.50e+03 9.79e-02 1.20e+02 pdb=" CG ASN A 98 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.170 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 100 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 101 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 99 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO B 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.037 5.00e-02 4.00e+02 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 157 2.66 - 3.22: 12297 3.22 - 3.78: 18514 3.78 - 4.34: 25186 4.34 - 4.90: 40198 Nonbonded interactions: 96352 Sorted by model distance: nonbonded pdb=" ND2 ASN A 90 " pdb=" C1 NAG A1302 " model vdw 2.096 3.550 nonbonded pdb=" OG1 THR A 198 " pdb=" OG SER A 343 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP A 742 " pdb=" NZ LYS A 747 " model vdw 2.172 3.120 nonbonded pdb=" NH1 ARG A 546 " pdb=" O LEU A 909 " model vdw 2.190 3.120 nonbonded pdb=" OG1 THR C 14 " pdb=" OG SER C 122 " model vdw 2.205 3.040 ... (remaining 96347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 : 0.005 0.177 12969 Z= 0.260 Angle : 0.941 43.380 17562 Z= 0.453 Chirality : 0.046 0.207 2008 Planarity : 0.006 0.113 2218 Dihedral : 10.230 81.253 4750 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.54 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.18), residues: 1618 helix: -1.47 (0.16), residues: 739 sheet: -1.26 (0.30), residues: 265 loop : -2.74 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1191 TYR 0.025 0.002 TYR C 33 PHE 0.027 0.002 PHE B 92 TRP 0.027 0.002 TRP C 112 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00505 (12962) covalent geometry : angle 0.80816 (17547) SS BOND : bond 0.00981 ( 6) SS BOND : angle 2.05716 ( 12) hydrogen bonds : bond 0.12804 ( 700) hydrogen bonds : angle 7.03471 ( 2028) link_NAG-ASN : bond 0.17703 ( 1) link_NAG-ASN : angle 36.68725 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8666 (mmt) cc_final: 0.8080 (mmt) REVERT: A 104 MET cc_start: 0.7078 (tmm) cc_final: 0.6857 (tmm) REVERT: A 742 ASP cc_start: 0.8908 (p0) cc_final: 0.8563 (p0) REVERT: A 802 TRP cc_start: 0.8825 (t60) cc_final: 0.8245 (t60) REVERT: A 947 MET cc_start: 0.7873 (tpp) cc_final: 0.7620 (tpp) REVERT: B 1 GLN cc_start: 0.8217 (mp10) cc_final: 0.7996 (mp10) REVERT: B 27 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8062 (tt0) REVERT: B 84 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 140 CYS cc_start: 0.6700 (m) cc_final: 0.6263 (m) REVERT: B 154 TRP cc_start: 0.7618 (m100) cc_final: 0.7352 (m100) REVERT: B 201 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 197 TRP cc_start: 0.7632 (t60) cc_final: 0.7349 (t60) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1339 time to fit residues: 45.7029 Evaluate side-chains 126 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 356 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 611 HIS A 628 GLN A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.187850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170762 restraints weight = 21150.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.167948 restraints weight = 39733.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168588 restraints weight = 39148.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168533 restraints weight = 24445.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168788 restraints weight = 22232.135| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12969 Z= 0.148 Angle : 0.675 12.780 17562 Z= 0.354 Chirality : 0.044 0.184 2008 Planarity : 0.005 0.089 2218 Dihedral : 7.221 62.941 1854 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.20), residues: 1618 helix: 0.08 (0.19), residues: 746 sheet: -0.76 (0.30), residues: 277 loop : -2.30 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1187 TYR 0.021 0.002 TYR C 33 PHE 0.022 0.002 PHE B 92 TRP 0.014 0.001 TRP C 112 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00306 (12962) covalent geometry : angle 0.67278 (17547) SS BOND : bond 0.00570 ( 6) SS BOND : angle 1.01366 ( 12) hydrogen bonds : bond 0.05652 ( 700) hydrogen bonds : angle 5.16898 ( 2028) link_NAG-ASN : bond 0.00627 ( 1) link_NAG-ASN : angle 4.00243 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7616 (ptp) cc_final: 0.7395 (ptm) REVERT: A 104 MET cc_start: 0.6607 (tmm) cc_final: 0.6374 (tmm) REVERT: A 234 ILE cc_start: 0.7690 (mt) cc_final: 0.7440 (mt) REVERT: A 489 TYR cc_start: 0.7158 (m-80) cc_final: 0.6921 (m-10) REVERT: A 802 TRP cc_start: 0.8788 (t60) cc_final: 0.8468 (t60) REVERT: A 887 LYS cc_start: 0.6730 (mmpt) cc_final: 0.6468 (tptp) REVERT: B 1 GLN cc_start: 0.7905 (mp10) cc_final: 0.7679 (mp10) REVERT: B 181 MET cc_start: 0.7860 (ptm) cc_final: 0.7428 (ttt) REVERT: B 185 LEU cc_start: 0.6770 (mp) cc_final: 0.6456 (tp) REVERT: B 201 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5582 (mt-10) outliers start: 3 outliers final: 0 residues processed: 196 average time/residue: 0.1005 time to fit residues: 29.5486 Evaluate side-chains 129 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 146 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 162 GLN B 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159741 restraints weight = 20920.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159582 restraints weight = 32286.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159871 restraints weight = 28232.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159496 restraints weight = 19170.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.160033 restraints weight = 18119.491| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12969 Z= 0.148 Angle : 0.643 13.500 17562 Z= 0.338 Chirality : 0.044 0.169 2008 Planarity : 0.005 0.083 2218 Dihedral : 6.697 55.566 1854 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1618 helix: 0.59 (0.19), residues: 754 sheet: -0.45 (0.30), residues: 276 loop : -2.00 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.017 0.002 TYR C 33 PHE 0.023 0.002 PHE B 92 TRP 0.021 0.002 TRP B 154 HIS 0.008 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00315 (12962) covalent geometry : angle 0.64108 (17547) SS BOND : bond 0.00706 ( 6) SS BOND : angle 1.07373 ( 12) hydrogen bonds : bond 0.05427 ( 700) hydrogen bonds : angle 4.84457 ( 2028) link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 3.89348 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8420 (tmm) cc_final: 0.8010 (tmm) REVERT: A 297 SER cc_start: 0.8070 (m) cc_final: 0.7377 (p) REVERT: A 947 MET cc_start: 0.8189 (tmm) cc_final: 0.7689 (tpp) REVERT: A 1164 TYR cc_start: 0.8073 (m-80) cc_final: 0.7818 (m-10) REVERT: B 154 TRP cc_start: 0.8234 (m100) cc_final: 0.7147 (m100) REVERT: C 205 ASN cc_start: 0.7534 (m110) cc_final: 0.6773 (m-40) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.0982 time to fit residues: 27.5612 Evaluate side-chains 126 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 154 optimal weight: 0.0020 chunk 138 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 0.0000 chunk 36 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160276 restraints weight = 19708.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157481 restraints weight = 33620.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157842 restraints weight = 35862.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156981 restraints weight = 25849.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157087 restraints weight = 26536.276| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12969 Z= 0.126 Angle : 0.611 11.393 17562 Z= 0.320 Chirality : 0.043 0.173 2008 Planarity : 0.004 0.081 2218 Dihedral : 6.379 54.451 1854 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1618 helix: 0.94 (0.19), residues: 754 sheet: -0.12 (0.31), residues: 278 loop : -1.82 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 114 TYR 0.021 0.001 TYR A 952 PHE 0.022 0.002 PHE A 207 TRP 0.014 0.001 TRP B 154 HIS 0.015 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00254 (12962) covalent geometry : angle 0.60855 (17547) SS BOND : bond 0.00563 ( 6) SS BOND : angle 1.04934 ( 12) hydrogen bonds : bond 0.05004 ( 700) hydrogen bonds : angle 4.60862 ( 2028) link_NAG-ASN : bond 0.00291 ( 1) link_NAG-ASN : angle 3.65320 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 MET cc_start: 0.8662 (tpt) cc_final: 0.8378 (tpp) REVERT: A 450 VAL cc_start: 0.7667 (t) cc_final: 0.7322 (m) REVERT: A 939 ILE cc_start: 0.8742 (tp) cc_final: 0.8108 (tp) REVERT: A 947 MET cc_start: 0.8005 (tmm) cc_final: 0.7672 (tpp) REVERT: B 154 TRP cc_start: 0.8059 (m100) cc_final: 0.7116 (m100) REVERT: C 205 ASN cc_start: 0.7449 (m110) cc_final: 0.6926 (m-40) REVERT: C 206 VAL cc_start: 0.8808 (t) cc_final: 0.8603 (t) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0990 time to fit residues: 27.3871 Evaluate side-chains 132 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 171 ASN A 586 HIS A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 130 GLN B 195 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154409 restraints weight = 19981.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151092 restraints weight = 29953.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149370 restraints weight = 25812.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148661 restraints weight = 23603.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149303 restraints weight = 22952.015| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12969 Z= 0.147 Angle : 0.631 11.354 17562 Z= 0.333 Chirality : 0.044 0.169 2008 Planarity : 0.004 0.077 2218 Dihedral : 6.193 52.598 1854 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1618 helix: 1.02 (0.19), residues: 753 sheet: -0.05 (0.31), residues: 279 loop : -1.75 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1146 TYR 0.015 0.001 TYR A 276 PHE 0.024 0.002 PHE B 92 TRP 0.016 0.001 TRP C 112 HIS 0.006 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00316 (12962) covalent geometry : angle 0.62789 (17547) SS BOND : bond 0.00915 ( 6) SS BOND : angle 1.61681 ( 12) hydrogen bonds : bond 0.05242 ( 700) hydrogen bonds : angle 4.57026 ( 2028) link_NAG-ASN : bond 0.00264 ( 1) link_NAG-ASN : angle 3.67358 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.7990 (m) cc_final: 0.7241 (p) REVERT: A 439 MET cc_start: 0.8891 (tpt) cc_final: 0.8613 (tpp) REVERT: A 453 ASP cc_start: 0.6866 (m-30) cc_final: 0.6533 (m-30) REVERT: A 939 ILE cc_start: 0.8692 (tp) cc_final: 0.8142 (tp) REVERT: A 947 MET cc_start: 0.8001 (tmm) cc_final: 0.7750 (tpp) REVERT: A 1183 ILE cc_start: 0.6971 (mt) cc_final: 0.6697 (mm) REVERT: B 86 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8542 (tm-30) REVERT: B 154 TRP cc_start: 0.8244 (m100) cc_final: 0.7138 (m100) REVERT: C 205 ASN cc_start: 0.7516 (m110) cc_final: 0.6978 (m-40) REVERT: C 206 VAL cc_start: 0.8874 (t) cc_final: 0.8657 (t) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.0964 time to fit residues: 27.3253 Evaluate side-chains 138 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 0.0370 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155568 restraints weight = 19493.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153758 restraints weight = 31768.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153749 restraints weight = 32410.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152315 restraints weight = 31585.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152701 restraints weight = 29408.768| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12969 Z= 0.126 Angle : 0.609 11.711 17562 Z= 0.319 Chirality : 0.043 0.224 2008 Planarity : 0.004 0.067 2218 Dihedral : 6.010 49.998 1854 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1618 helix: 1.19 (0.19), residues: 757 sheet: 0.12 (0.31), residues: 277 loop : -1.67 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.019 0.001 TYR A 927 PHE 0.024 0.001 PHE A 203 TRP 0.010 0.001 TRP B 102 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00256 (12962) covalent geometry : angle 0.60624 (17547) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.17116 ( 12) hydrogen bonds : bond 0.04951 ( 700) hydrogen bonds : angle 4.44211 ( 2028) link_NAG-ASN : bond 0.00319 ( 1) link_NAG-ASN : angle 3.53403 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 THR cc_start: 0.7934 (m) cc_final: 0.7251 (t) REVERT: A 439 MET cc_start: 0.8941 (tpt) cc_final: 0.8724 (tpp) REVERT: A 939 ILE cc_start: 0.8602 (tp) cc_final: 0.8034 (tp) REVERT: A 1156 PHE cc_start: 0.7070 (t80) cc_final: 0.5676 (m-80) REVERT: B 86 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 140 CYS cc_start: 0.6643 (m) cc_final: 0.6145 (m) REVERT: B 154 TRP cc_start: 0.8106 (m100) cc_final: 0.7098 (m100) REVERT: C 205 ASN cc_start: 0.7501 (m110) cc_final: 0.6897 (m-40) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0981 time to fit residues: 27.4339 Evaluate side-chains 127 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 110 optimal weight: 0.0370 overall best weight: 0.4672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157438 restraints weight = 19427.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152892 restraints weight = 27804.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150309 restraints weight = 30884.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150242 restraints weight = 32017.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150953 restraints weight = 26760.500| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12969 Z= 0.121 Angle : 0.599 11.690 17562 Z= 0.311 Chirality : 0.043 0.202 2008 Planarity : 0.004 0.066 2218 Dihedral : 5.886 48.224 1854 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1618 helix: 1.32 (0.19), residues: 756 sheet: 0.42 (0.32), residues: 267 loop : -1.67 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1221 TYR 0.015 0.001 TYR A 927 PHE 0.018 0.001 PHE B 92 TRP 0.010 0.001 TRP B 154 HIS 0.002 0.000 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00241 (12962) covalent geometry : angle 0.59687 (17547) SS BOND : bond 0.00384 ( 6) SS BOND : angle 0.83536 ( 12) hydrogen bonds : bond 0.04695 ( 700) hydrogen bonds : angle 4.30254 ( 2028) link_NAG-ASN : bond 0.00238 ( 1) link_NAG-ASN : angle 3.28300 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7394 (m) cc_final: 0.6980 (t) REVERT: A 434 THR cc_start: 0.8074 (m) cc_final: 0.7447 (t) REVERT: A 939 ILE cc_start: 0.8665 (tp) cc_final: 0.8112 (tp) REVERT: A 1156 PHE cc_start: 0.7343 (t80) cc_final: 0.5518 (m-80) REVERT: B 140 CYS cc_start: 0.6609 (m) cc_final: 0.6085 (m) REVERT: B 154 TRP cc_start: 0.8361 (m100) cc_final: 0.7258 (m100) REVERT: C 205 ASN cc_start: 0.7324 (m110) cc_final: 0.6648 (m-40) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0922 time to fit residues: 24.7770 Evaluate side-chains 125 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156034 restraints weight = 19292.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153831 restraints weight = 29390.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153455 restraints weight = 31801.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151976 restraints weight = 29991.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152763 restraints weight = 28052.921| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12969 Z= 0.127 Angle : 0.617 11.862 17562 Z= 0.321 Chirality : 0.044 0.250 2008 Planarity : 0.004 0.086 2218 Dihedral : 5.884 48.683 1854 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1618 helix: 1.31 (0.19), residues: 756 sheet: 0.28 (0.32), residues: 277 loop : -1.57 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1084 TYR 0.041 0.001 TYR B 146 PHE 0.020 0.001 PHE A 78 TRP 0.010 0.001 TRP A 231 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00259 (12962) covalent geometry : angle 0.61528 (17547) SS BOND : bond 0.00903 ( 6) SS BOND : angle 1.19552 ( 12) hydrogen bonds : bond 0.04742 ( 700) hydrogen bonds : angle 4.35491 ( 2028) link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 3.09271 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7233 (m) cc_final: 0.6869 (t) REVERT: A 434 THR cc_start: 0.8076 (m) cc_final: 0.7554 (t) REVERT: A 939 ILE cc_start: 0.8765 (tp) cc_final: 0.8174 (tp) REVERT: A 947 MET cc_start: 0.7799 (tmm) cc_final: 0.6958 (tpp) REVERT: B 154 TRP cc_start: 0.8409 (m100) cc_final: 0.7007 (m100) REVERT: C 205 ASN cc_start: 0.7348 (m110) cc_final: 0.6644 (m-40) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0907 time to fit residues: 24.4879 Evaluate side-chains 127 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153530 restraints weight = 19539.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151711 restraints weight = 33290.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150916 restraints weight = 31649.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148249 restraints weight = 33820.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149155 restraints weight = 31646.494| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12969 Z= 0.131 Angle : 0.629 11.921 17562 Z= 0.328 Chirality : 0.044 0.256 2008 Planarity : 0.004 0.085 2218 Dihedral : 5.883 49.197 1854 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1618 helix: 1.23 (0.19), residues: 762 sheet: 0.22 (0.31), residues: 278 loop : -1.61 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.018 0.001 TYR A 306 PHE 0.029 0.002 PHE A 207 TRP 0.013 0.001 TRP C 112 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00274 (12962) covalent geometry : angle 0.62685 (17547) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.50364 ( 12) hydrogen bonds : bond 0.04908 ( 700) hydrogen bonds : angle 4.39015 ( 2028) link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 2.92316 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7228 (m) cc_final: 0.6849 (t) REVERT: A 74 MET cc_start: 0.8320 (tmm) cc_final: 0.8020 (tmm) REVERT: A 434 THR cc_start: 0.8224 (m) cc_final: 0.7717 (t) REVERT: A 939 ILE cc_start: 0.8754 (tp) cc_final: 0.8153 (tp) REVERT: A 947 MET cc_start: 0.7988 (tmm) cc_final: 0.7204 (tpp) REVERT: B 154 TRP cc_start: 0.8146 (m100) cc_final: 0.7221 (m100) REVERT: B 198 TYR cc_start: 0.6184 (m-80) cc_final: 0.5810 (m-80) REVERT: C 205 ASN cc_start: 0.7363 (m110) cc_final: 0.6628 (m-40) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0912 time to fit residues: 24.9509 Evaluate side-chains 126 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 0.0060 chunk 151 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158628 restraints weight = 21119.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155826 restraints weight = 36165.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156173 restraints weight = 38260.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155122 restraints weight = 28054.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155426 restraints weight = 26141.531| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12969 Z= 0.142 Angle : 0.647 12.160 17562 Z= 0.338 Chirality : 0.044 0.248 2008 Planarity : 0.004 0.082 2218 Dihedral : 5.902 49.443 1854 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1618 helix: 1.22 (0.19), residues: 759 sheet: 0.19 (0.31), residues: 281 loop : -1.47 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.024 0.001 TYR A 306 PHE 0.024 0.002 PHE A 710 TRP 0.011 0.001 TRP A 231 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00308 (12962) covalent geometry : angle 0.64538 (17547) SS BOND : bond 0.00444 ( 6) SS BOND : angle 1.35545 ( 12) hydrogen bonds : bond 0.05064 ( 700) hydrogen bonds : angle 4.43018 ( 2028) link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 2.84059 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASN cc_start: 0.7377 (m-40) cc_final: 0.6936 (p0) REVERT: A 434 THR cc_start: 0.8320 (m) cc_final: 0.7801 (t) REVERT: A 513 MET cc_start: 0.3749 (tmm) cc_final: 0.3491 (tmm) REVERT: A 939 ILE cc_start: 0.8758 (tp) cc_final: 0.8175 (tp) REVERT: A 947 MET cc_start: 0.7978 (tmm) cc_final: 0.7202 (tpp) REVERT: B 140 CYS cc_start: 0.6618 (m) cc_final: 0.5943 (m) REVERT: B 154 TRP cc_start: 0.8367 (m100) cc_final: 0.6942 (m100) REVERT: B 198 TYR cc_start: 0.6401 (m-80) cc_final: 0.5889 (m-80) REVERT: C 205 ASN cc_start: 0.7347 (m110) cc_final: 0.6699 (m-40) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0909 time to fit residues: 24.5072 Evaluate side-chains 123 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 53 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.170870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158707 restraints weight = 21024.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.155951 restraints weight = 35112.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153864 restraints weight = 32136.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153628 restraints weight = 31716.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153165 restraints weight = 28127.908| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12969 Z= 0.150 Angle : 0.666 12.259 17562 Z= 0.348 Chirality : 0.045 0.256 2008 Planarity : 0.005 0.083 2218 Dihedral : 6.000 49.630 1854 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1618 helix: 1.17 (0.19), residues: 760 sheet: 0.10 (0.31), residues: 287 loop : -1.45 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.023 0.002 TYR A 49 PHE 0.025 0.002 PHE B 92 TRP 0.019 0.002 TRP B 154 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (12962) covalent geometry : angle 0.66433 (17547) SS BOND : bond 0.00539 ( 6) SS BOND : angle 1.17191 ( 12) hydrogen bonds : bond 0.05389 ( 700) hydrogen bonds : angle 4.52055 ( 2028) link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 2.78184 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.34 seconds wall clock time: 31 minutes 10.73 seconds (1870.73 seconds total)