Starting phenix.real_space_refine on Sat Sep 12 02:12:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6fn4_4282/09_2026/6fn4_4282.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fn4_4282/09_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_4282/09_2026/6fn4_4282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fn4_4282/09_2026/6fn4_4282.map" model { file = "/net/cci-nas-00/data/ceres_data/6fn4_4282/09_2026/6fn4_4282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fn4_4282/09_2026/6fn4_4282.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6fn4_4282/09_2026/6fn4_4282.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6fn4_4282/09_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-2.2.1-6174/lib/python3.11/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 chiralities: 3 Time building chain proxies: 2.37, per 1000 atoms: 0.19 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: 1.06 Conformation dependent library (CDL) restraints added in 450.2 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: 0.40 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: 2.51 Time building geometry restraints manager: 1.37 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: 7311 16.25 - 32.50: 307 32.50 - 48.75: 62 48.75 - 65.00: 4 65.00 - 81.25: 7 Dihedral angle restraints: 7691 sinusoidal: 3014 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 7688 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.440 Find NCS groups from input model: 0.080 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 9.969 81.253 4675 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/Z covalent geometry : bond 0.00505 / 0.25 (12962) covalent geometry : angle 0.80816 / 0.42 (17547) SS BOND : bond 0.00981 / 0.63 ( 6) SS BOND : angle 2.05716 / 1.40 ( 12) hydrogen bonds : bond 0.12804 / 8.39 ( 700) hydrogen bonds : angle 7.03471 / 5.02 ( 2028) link_NAG-ASN : bond 0.17703 / 11.80 ( 1) link_NAG-ASN : angle 36.68725 / 24.46 ( 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 : 0.473 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: 0.1191 time to fit residues: 41.0027 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 : 0.501 ------------------------------------------------------------------------------- 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... 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** B 195 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.186744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164595 restraints weight = 20734.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164054 restraints weight = 35693.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164967 restraints weight = 28886.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164269 restraints weight = 19531.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164945 restraints weight = 18719.893| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2218 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= 0.161 Angle : 0.670 12.084 17562 Z= 0.353 Chirality : 0.044 0.182 2008 Planarity : 0.005 0.090 2218 Dihedral : 6.393 59.623 1779 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % 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: -1.46 (0.20), residues: 1618 helix: 0.03 (0.18), residues: 753 sheet: -0.80 (0.30), residues: 277 loop : -2.31 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1187 TYR 0.021 0.002 TYR C 33 PHE 0.023 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/Z covalent geometry : bond 0.00312 / 0.16 (12962) covalent geometry : angle 0.66732 / 0.35 (17547) SS BOND : bond 0.00588 / 0.37 ( 6) SS BOND : angle 1.03589 / 0.69 ( 12) hydrogen bonds : bond 0.05750 / 3.85 ( 700) hydrogen bonds : angle 5.26104 / 3.77 ( 2028) link_NAG-ASN : bond 0.00718 / 0.48 ( 1) link_NAG-ASN : angle 4.53071 / 3.62 ( 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 190 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7703 (ptp) cc_final: 0.7464 (ptm) REVERT: A 104 MET cc_start: 0.6689 (tmm) cc_final: 0.6457 (tmm) REVERT: A 234 ILE cc_start: 0.7691 (mt) cc_final: 0.7430 (mt) REVERT: A 489 TYR cc_start: 0.7211 (m-80) cc_final: 0.6778 (m-10) REVERT: A 802 TRP cc_start: 0.8791 (t60) cc_final: 0.8449 (t60) REVERT: A 887 LYS cc_start: 0.6714 (mmpt) cc_final: 0.6424 (tptp) REVERT: A 936 VAL cc_start: 0.8121 (p) cc_final: 0.7898 (t) REVERT: B 1 GLN cc_start: 0.7963 (mp10) cc_final: 0.7728 (mp10) REVERT: B 181 MET cc_start: 0.7926 (ptm) cc_final: 0.7373 (ttt) REVERT: B 185 LEU cc_start: 0.6808 (mp) cc_final: 0.6483 (tp) REVERT: B 201 GLU cc_start: 0.6029 (mt-10) cc_final: 0.5676 (mt-10) REVERT: C 205 ASN cc_start: 0.7765 (m110) cc_final: 0.7535 (m-40) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1025 time to fit residues: 29.2200 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 : 0.452 ------------------------------------------------------------------------------- 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: 0.9980 chunk 131 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153989 restraints weight = 20022.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150241 restraints weight = 32434.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149012 restraints weight = 33588.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147934 restraints weight = 34349.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148692 restraints weight = 27945.360| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12969 Z= 0.175 Angle : 0.691 13.792 17562 Z= 0.363 Chirality : 0.046 0.181 2008 Planarity : 0.005 0.084 2218 Dihedral : 6.116 58.218 1779 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 0.22 % Allowed : 5.05 % Favored : 94.73 % 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: -0.90 (0.20), residues: 1618 helix: 0.46 (0.19), residues: 753 sheet: -0.52 (0.30), residues: 281 loop : -2.00 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 441 TYR 0.018 0.002 TYR C 33 PHE 0.029 0.002 PHE A 956 TRP 0.027 0.002 TRP B 154 HIS 0.011 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (12962) covalent geometry : angle 0.68856 / 0.36 (17547) SS BOND : bond 0.00623 / 0.41 ( 6) SS BOND : angle 1.25860 / 0.81 ( 12) hydrogen bonds : bond 0.05849 / 3.89 ( 700) hydrogen bonds : angle 4.95688 / 3.56 ( 2028) link_NAG-ASN : bond 0.00159 / 0.11 ( 1) link_NAG-ASN : angle 4.16285 / 3.21 ( 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 183 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8936 (mmm) cc_final: 0.8688 (mmm) REVERT: A 88 MET cc_start: 0.7678 (ptp) cc_final: 0.7477 (ptm) REVERT: A 297 SER cc_start: 0.8094 (m) cc_final: 0.7385 (p) REVERT: A 496 MET cc_start: 0.3877 (ttm) cc_final: 0.3585 (mmm) REVERT: A 947 MET cc_start: 0.8189 (tmm) cc_final: 0.7812 (tpp) REVERT: A 1164 TYR cc_start: 0.8205 (m-80) cc_final: 0.7985 (m-10) REVERT: B 154 TRP cc_start: 0.8311 (m100) cc_final: 0.7421 (m100) REVERT: C 205 ASN cc_start: 0.7753 (m110) cc_final: 0.7245 (m-40) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.1035 time to fit residues: 27.9495 Evaluate side-chains 128 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 HIS ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141602 restraints weight = 20300.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138615 restraints weight = 34717.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136086 restraints weight = 36489.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135693 restraints weight = 38528.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135990 restraints weight = 28524.432| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12969 Z= 0.243 Angle : 0.811 13.452 17562 Z= 0.428 Chirality : 0.050 0.247 2008 Planarity : 0.006 0.097 2218 Dihedral : 6.461 51.315 1779 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 0.37 % Allowed : 5.20 % Favored : 94.44 % 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: -0.99 (0.20), residues: 1618 helix: 0.33 (0.19), residues: 746 sheet: -0.41 (0.30), residues: 284 loop : -2.02 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 546 TYR 0.033 0.003 TYR A 49 PHE 0.043 0.003 PHE A 313 TRP 0.021 0.002 TRP B 102 HIS 0.015 0.002 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (12962) covalent geometry : angle 0.80887 / 0.43 (17547) SS BOND : bond 0.00810 / 0.50 ( 6) SS BOND : angle 1.55378 / 0.99 ( 12) hydrogen bonds : bond 0.06908 / 4.59 ( 700) hydrogen bonds : angle 5.24029 / 3.75 ( 2028) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 3.89012 / 2.98 ( 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 173 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8377 (tmm) cc_final: 0.8068 (tmm) REVERT: A 185 ILE cc_start: 0.9028 (tp) cc_final: 0.8816 (tp) REVERT: A 203 PHE cc_start: 0.7749 (t80) cc_final: 0.7524 (t80) REVERT: A 297 SER cc_start: 0.7911 (m) cc_final: 0.7116 (p) REVERT: A 434 THR cc_start: 0.8415 (m) cc_final: 0.7870 (t) REVERT: A 496 MET cc_start: 0.5524 (ttm) cc_final: 0.5204 (tpp) REVERT: A 802 TRP cc_start: 0.8913 (t60) cc_final: 0.8321 (t60) REVERT: A 947 MET cc_start: 0.8118 (tmm) cc_final: 0.7827 (tpp) REVERT: A 948 MET cc_start: 0.8994 (tmm) cc_final: 0.8589 (tmm) REVERT: B 86 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8773 (tm-30) REVERT: B 95 GLN cc_start: 0.7927 (tp40) cc_final: 0.7541 (tp40) outliers start: 5 outliers final: 0 residues processed: 172 average time/residue: 0.0965 time to fit residues: 25.0388 Evaluate side-chains 130 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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: 0.9980 chunk 138 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 0.0070 chunk 134 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161165 restraints weight = 21286.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155548 restraints weight = 38080.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152878 restraints weight = 33704.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152050 restraints weight = 38225.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152853 restraints weight = 28909.058| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4991 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= 0.134 Angle : 0.633 12.812 17562 Z= 0.330 Chirality : 0.044 0.203 2008 Planarity : 0.004 0.080 2218 Dihedral : 5.908 47.261 1779 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -0.49 (0.21), residues: 1618 helix: 0.80 (0.19), residues: 748 sheet: -0.23 (0.30), residues: 279 loop : -1.82 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1221 TYR 0.014 0.001 TYR C 33 PHE 0.019 0.002 PHE B 92 TRP 0.016 0.001 TRP B 154 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (12962) covalent geometry : angle 0.63121 / 0.33 (17547) SS BOND : bond 0.00911 / 0.48 ( 6) SS BOND : angle 1.26702 / 0.82 ( 12) hydrogen bonds : bond 0.05501 / 3.68 ( 700) hydrogen bonds : angle 4.67356 / 3.37 ( 2028) link_NAG-ASN : bond 0.00112 / 0.07 ( 1) link_NAG-ASN : angle 3.53919 / 2.77 ( 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 194 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.8098 (m) cc_final: 0.7349 (p) REVERT: A 434 THR cc_start: 0.8442 (m) cc_final: 0.7920 (t) REVERT: A 518 GLN cc_start: 0.7303 (mt0) cc_final: 0.6544 (mp10) REVERT: A 947 MET cc_start: 0.8163 (tmm) cc_final: 0.7821 (tpp) REVERT: B 86 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8643 (tm-30) REVERT: B 95 GLN cc_start: 0.7216 (tp40) cc_final: 0.6850 (tp40) REVERT: B 154 TRP cc_start: 0.8329 (m100) cc_final: 0.7128 (m100) REVERT: C 205 ASN cc_start: 0.7724 (m110) cc_final: 0.7446 (m-40) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1000 time to fit residues: 29.0646 Evaluate side-chains 140 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 0.1980 chunk 14 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.0020 chunk 96 optimal weight: 8.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN A 536 GLN 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159276 restraints weight = 21022.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156760 restraints weight = 34153.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156268 restraints weight = 31679.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155261 restraints weight = 27523.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155545 restraints weight = 26955.068| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5300 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= 0.128 Angle : 0.629 11.864 17562 Z= 0.327 Chirality : 0.044 0.265 2008 Planarity : 0.004 0.074 2218 Dihedral : 5.675 49.172 1779 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.36 % 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: -0.24 (0.21), residues: 1618 helix: 1.01 (0.19), residues: 757 sheet: -0.11 (0.30), residues: 278 loop : -1.73 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 576 TYR 0.025 0.001 TYR A 309 PHE 0.026 0.001 PHE A 758 TRP 0.015 0.001 TRP B 154 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (12962) covalent geometry : angle 0.62622 / 0.33 (17547) SS BOND : bond 0.00417 / 0.27 ( 6) SS BOND : angle 1.53183 / 0.90 ( 12) hydrogen bonds : bond 0.05065 / 3.40 ( 700) hydrogen bonds : angle 4.55525 / 3.28 ( 2028) link_NAG-ASN : bond 0.00095 / 0.06 ( 1) link_NAG-ASN : angle 3.47316 / 2.72 ( 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 192 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.8129 (m) cc_final: 0.7365 (p) REVERT: A 305 ILE cc_start: 0.8920 (tp) cc_final: 0.8716 (tt) REVERT: A 434 THR cc_start: 0.8243 (m) cc_final: 0.7801 (t) REVERT: A 518 GLN cc_start: 0.7310 (mt0) cc_final: 0.6633 (mp10) REVERT: A 707 TRP cc_start: 0.8513 (p-90) cc_final: 0.8278 (p-90) REVERT: A 802 TRP cc_start: 0.8926 (t60) cc_final: 0.8316 (t60) REVERT: A 947 MET cc_start: 0.8112 (tmm) cc_final: 0.7629 (tpp) REVERT: B 86 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8565 (tm-30) REVERT: B 154 TRP cc_start: 0.8146 (m100) cc_final: 0.7238 (m100) REVERT: C 197 TRP cc_start: 0.7299 (t60) cc_final: 0.7097 (t60) REVERT: C 205 ASN cc_start: 0.7612 (m110) cc_final: 0.7235 (m-40) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.0878 time to fit residues: 26.1769 Evaluate side-chains 140 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 60 optimal weight: 0.0870 chunk 110 optimal weight: 7.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161851 restraints weight = 21173.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157217 restraints weight = 31132.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154974 restraints weight = 30906.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154853 restraints weight = 33916.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154996 restraints weight = 28903.847| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12969 Z= 0.123 Angle : 0.611 11.501 17562 Z= 0.317 Chirality : 0.043 0.181 2008 Planarity : 0.004 0.069 2218 Dihedral : 5.464 50.933 1779 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.67 % 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: 0.00 (0.21), residues: 1618 helix: 1.15 (0.19), residues: 758 sheet: 0.25 (0.31), residues: 268 loop : -1.65 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1046 TYR 0.022 0.001 TYR A 309 PHE 0.022 0.001 PHE A 238 TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (12962) covalent geometry : angle 0.60889 / 0.32 (17547) SS BOND : bond 0.00438 / 0.29 ( 6) SS BOND : angle 1.42052 / 0.93 ( 12) hydrogen bonds : bond 0.04810 / 3.23 ( 700) hydrogen bonds : angle 4.41214 / 3.18 ( 2028) link_NAG-ASN : bond 0.00119 / 0.08 ( 1) link_NAG-ASN : angle 3.27003 / 2.57 ( 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 189 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASN cc_start: 0.7245 (m-40) cc_final: 0.6710 (p0) REVERT: A 434 THR cc_start: 0.8382 (m) cc_final: 0.7970 (t) REVERT: A 518 GLN cc_start: 0.7497 (mt0) cc_final: 0.6645 (mp10) REVERT: A 947 MET cc_start: 0.8164 (tmm) cc_final: 0.7698 (tpp) REVERT: A 1089 MET cc_start: 0.6410 (pmm) cc_final: 0.6192 (pmm) REVERT: B 140 CYS cc_start: 0.6860 (m) cc_final: 0.6643 (m) REVERT: B 154 TRP cc_start: 0.8405 (m100) cc_final: 0.7260 (m100) REVERT: C 197 TRP cc_start: 0.7430 (t60) cc_final: 0.7176 (t60) REVERT: C 205 ASN cc_start: 0.7540 (m110) cc_final: 0.7099 (m-40) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0921 time to fit residues: 27.0302 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 : 0.484 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 157 optimal weight: 0.9980 chunk 145 optimal weight: 0.0570 chunk 130 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160762 restraints weight = 20834.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158461 restraints weight = 36571.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157965 restraints weight = 33923.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155963 restraints weight = 32410.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156319 restraints weight = 29427.774| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12969 Z= 0.122 Angle : 0.617 11.402 17562 Z= 0.320 Chirality : 0.043 0.177 2008 Planarity : 0.004 0.068 2218 Dihedral : 5.412 52.767 1779 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 0.12 (0.21), residues: 1618 helix: 1.25 (0.19), residues: 757 sheet: 0.25 (0.32), residues: 272 loop : -1.56 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1046 TYR 0.021 0.001 TYR A 309 PHE 0.021 0.001 PHE A 758 TRP 0.020 0.001 TRP B 154 HIS 0.003 0.000 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (12962) covalent geometry : angle 0.61491 / 0.32 (17547) SS BOND : bond 0.00421 / 0.27 ( 6) SS BOND : angle 1.10332 / 0.72 ( 12) hydrogen bonds : bond 0.04690 / 3.17 ( 700) hydrogen bonds : angle 4.39252 / 3.19 ( 2028) link_NAG-ASN : bond 0.00117 / 0.08 ( 1) link_NAG-ASN : angle 3.12410 / 2.46 ( 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 179 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7277 (t80) cc_final: 0.7062 (t80) REVERT: A 432 LYS cc_start: 0.4913 (pttt) cc_final: 0.4501 (pttt) REVERT: A 496 MET cc_start: 0.5711 (mmm) cc_final: 0.5366 (tpp) REVERT: A 518 GLN cc_start: 0.7494 (mt0) cc_final: 0.6704 (mp10) REVERT: A 947 MET cc_start: 0.7946 (tmm) cc_final: 0.7202 (tpp) REVERT: A 1089 MET cc_start: 0.6405 (pmm) cc_final: 0.6172 (pmm) REVERT: C 197 TRP cc_start: 0.7417 (t60) cc_final: 0.7174 (t60) REVERT: C 205 ASN cc_start: 0.7397 (m110) cc_final: 0.6920 (m-40) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0890 time to fit residues: 24.6821 Evaluate side-chains 134 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 42 optimal weight: 0.0050 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.0070 chunk 28 optimal weight: 0.5980 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** 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 = 0.4079 r_free = 0.4079 target = 0.176582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161513 restraints weight = 21123.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158910 restraints weight = 37260.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158335 restraints weight = 28920.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157756 restraints weight = 24180.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158064 restraints weight = 20503.551| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12969 Z= 0.121 Angle : 0.616 11.308 17562 Z= 0.318 Chirality : 0.043 0.178 2008 Planarity : 0.004 0.066 2218 Dihedral : 5.329 54.273 1779 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 1.24 (0.19), residues: 759 sheet: 0.55 (0.32), residues: 262 loop : -1.61 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1084 TYR 0.036 0.001 TYR A 246 PHE 0.019 0.001 PHE A1085 TRP 0.017 0.001 TRP B 154 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (12962) covalent geometry : angle 0.61474 / 0.32 (17547) SS BOND : bond 0.00480 / 0.28 ( 6) SS BOND : angle 1.08130 / 0.66 ( 12) hydrogen bonds : bond 0.04553 / 3.07 ( 700) hydrogen bonds : angle 4.34114 / 3.15 ( 2028) link_NAG-ASN : bond 0.00151 / 0.10 ( 1) link_NAG-ASN : angle 2.98365 / 2.35 ( 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 : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7576 (m) cc_final: 0.7215 (t) REVERT: A 434 THR cc_start: 0.8136 (m) cc_final: 0.7541 (t) REVERT: A 518 GLN cc_start: 0.7539 (mt0) cc_final: 0.6710 (mp10) REVERT: A 519 PHE cc_start: 0.7052 (m-80) cc_final: 0.6797 (m-80) REVERT: A 769 PHE cc_start: 0.7770 (t80) cc_final: 0.7377 (t80) REVERT: A 802 TRP cc_start: 0.8909 (t60) cc_final: 0.8404 (t60) REVERT: A 947 MET cc_start: 0.7995 (tmm) cc_final: 0.7309 (tpp) REVERT: A 1055 LEU cc_start: 0.6841 (tp) cc_final: 0.6630 (mp) REVERT: A 1089 MET cc_start: 0.6556 (pmm) cc_final: 0.6322 (pmm) REVERT: B 154 TRP cc_start: 0.8412 (m100) cc_final: 0.7317 (m100) REVERT: C 197 TRP cc_start: 0.7452 (t60) cc_final: 0.7232 (t60) REVERT: C 205 ASN cc_start: 0.7337 (m110) cc_final: 0.6808 (m-40) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0944 time to fit residues: 25.6730 Evaluate side-chains 139 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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: 2.9990 chunk 91 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** 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 = 0.4043 r_free = 0.4043 target = 0.173211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158976 restraints weight = 21252.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156034 restraints weight = 34715.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156484 restraints weight = 35703.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155565 restraints weight = 27823.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155611 restraints weight = 27628.787| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12969 Z= 0.131 Angle : 0.642 11.417 17562 Z= 0.332 Chirality : 0.043 0.174 2008 Planarity : 0.004 0.068 2218 Dihedral : 5.370 55.504 1779 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.18 (0.19), residues: 760 sheet: 0.27 (0.32), residues: 278 loop : -1.52 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.021 0.001 TYR A 309 PHE 0.028 0.001 PHE A1085 TRP 0.014 0.001 TRP A 707 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12962) covalent geometry : angle 0.63999 / 0.33 (17547) SS BOND : bond 0.00438 / 0.29 ( 6) SS BOND : angle 1.13576 / 0.74 ( 12) hydrogen bonds : bond 0.04860 / 3.28 ( 700) hydrogen bonds : angle 4.43381 / 3.21 ( 2028) link_NAG-ASN : bond 0.00106 / 0.07 ( 1) link_NAG-ASN : angle 2.92284 / 2.29 ( 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 177 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 THR cc_start: 0.8254 (m) cc_final: 0.7807 (t) REVERT: A 518 GLN cc_start: 0.7455 (mt0) cc_final: 0.6869 (mp10) REVERT: A 802 TRP cc_start: 0.8938 (t60) cc_final: 0.8520 (t60) REVERT: A 947 MET cc_start: 0.7857 (tmm) cc_final: 0.7118 (tpp) REVERT: A 1089 MET cc_start: 0.6627 (pmm) cc_final: 0.6373 (pmm) REVERT: B 181 MET cc_start: 0.8590 (ppp) cc_final: 0.8320 (ppp) REVERT: C 197 TRP cc_start: 0.7488 (t60) cc_final: 0.7254 (t60) REVERT: C 205 ASN cc_start: 0.7387 (m110) cc_final: 0.6890 (m-40) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0953 time to fit residues: 26.2018 Evaluate side-chains 130 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 3.9990 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** 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 = 0.4009 r_free = 0.4009 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151636 restraints weight = 21181.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149310 restraints weight = 34494.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150202 restraints weight = 31629.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149621 restraints weight = 22290.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149758 restraints weight = 24109.263| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12969 Z= 0.147 Angle : 0.657 11.469 17562 Z= 0.342 Chirality : 0.044 0.217 2008 Planarity : 0.004 0.070 2218 Dihedral : 5.467 56.106 1779 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 0.02 (0.21), residues: 1618 helix: 1.07 (0.19), residues: 765 sheet: 0.35 (0.31), residues: 276 loop : -1.59 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1191 TYR 0.036 0.001 TYR A 246 PHE 0.027 0.002 PHE A1085 TRP 0.014 0.001 TRP B 154 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (12962) covalent geometry : angle 0.65571 / 0.34 (17547) SS BOND : bond 0.00508 / 0.32 ( 6) SS BOND : angle 1.29227 / 0.83 ( 12) hydrogen bonds : bond 0.05193 / 3.49 ( 700) hydrogen bonds : angle 4.54468 / 3.26 ( 2028) link_NAG-ASN : bond 0.00089 / 0.06 ( 1) link_NAG-ASN : angle 2.90486 / 2.27 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1769.48 seconds wall clock time: 31 minutes 31.92 seconds (1891.92 seconds total)