Starting phenix.real_space_refine on Thu Jul 31 03:12:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fn4_4282/07_2025/6fn4_4282.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fn4_4282/07_2025/6fn4_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_4282/07_2025/6fn4_4282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fn4_4282/07_2025/6fn4_4282.map" model { file = "/net/cci-nas-00/data/ceres_data/6fn4_4282/07_2025/6fn4_4282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fn4_4282/07_2025/6fn4_4282.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12702 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9182 Classifications: {'peptide': 1181} Link IDs: {'CIS': 5, 'PTRANS': 27, 'TRANS': 1148} Chain breaks: 1 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 207} Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'3PE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.89, per 1000 atoms: 0.62 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.94 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: 5.19 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2062 1.29 - 1.43: 3355 1.43 - 1.57: 7460 1.57 - 1.71: 2 1.71 - 1.84: 83 Bond restraints: 12962 Sorted by residual: bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.491 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.470 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.346 1.469 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 12957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 17485 4.50 - 9.01: 54 9.01 - 13.51: 7 13.51 - 18.02: 0 18.02 - 22.52: 1 Bond angle restraints: 17547 Sorted by residual: angle pdb=" O12 3PE A1304 " pdb=" P 3PE A1304 " pdb=" O14 3PE A1304 " ideal model delta sigma weight residual 123.79 101.27 22.52 3.00e+00 1.11e-01 5.64e+01 angle pdb=" C ASP A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta sigma weight residual 121.70 133.19 -11.49 1.80e+00 3.09e-01 4.07e+01 angle pdb=" C SER A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta sigma weight residual 121.70 131.52 -9.82 1.80e+00 3.09e-01 2.98e+01 angle pdb=" C VAL A 33 " pdb=" N SER A 34 " pdb=" CA SER A 34 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.98e+01 angle pdb=" C3 NAG A1302 " pdb=" C2 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 110.74 98.23 12.51 3.00e+00 1.11e-01 1.74e+01 ... (remaining 17542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 7365 16.25 - 32.50: 318 32.50 - 48.75: 69 48.75 - 65.00: 7 65.00 - 81.25: 7 Dihedral angle restraints: 7766 sinusoidal: 3089 harmonic: 4677 Sorted by residual: dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A1203 " pdb=" CB CYS A1203 " ideal model delta sinusoidal sigma weight residual -86.00 -159.27 73.27 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA ARG A 488 " pdb=" C ARG A 488 " pdb=" N TYR A 489 " pdb=" CA TYR A 489 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLY C 153 " pdb=" C GLY C 153 " pdb=" N TYR C 154 " pdb=" CA TYR C 154 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1362 0.041 - 0.083: 476 0.083 - 0.124: 142 0.124 - 0.166: 27 0.166 - 0.207: 1 Chirality restraints: 2008 Sorted by residual: chirality pdb=" CB ILE A 97 " pdb=" CA ILE A 97 " pdb=" CG1 ILE A 97 " pdb=" CG2 ILE A 97 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 839 " pdb=" CA ILE A 839 " pdb=" CG1 ILE A 839 " pdb=" CG2 ILE A 839 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 2005 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.062 2.00e-02 2.50e+03 9.79e-02 1.20e+02 pdb=" CG ASN A 98 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.170 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 100 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 101 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 99 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO B 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.037 5.00e-02 4.00e+02 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 157 2.66 - 3.22: 12297 3.22 - 3.78: 18514 3.78 - 4.34: 25186 4.34 - 4.90: 40198 Nonbonded interactions: 96352 Sorted by model distance: nonbonded pdb=" ND2 ASN A 90 " pdb=" C1 NAG A1302 " model vdw 2.096 3.550 nonbonded pdb=" OG1 THR A 198 " pdb=" OG SER A 343 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP A 742 " pdb=" NZ LYS A 747 " model vdw 2.172 3.120 nonbonded pdb=" NH1 ARG A 546 " pdb=" O LEU A 909 " model vdw 2.190 3.120 nonbonded pdb=" OG1 THR C 14 " pdb=" OG SER C 122 " model vdw 2.205 3.040 ... (remaining 96347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 12969 Z= 0.260 Angle : 0.941 43.380 17562 Z= 0.453 Chirality : 0.046 0.207 2008 Planarity : 0.006 0.113 2218 Dihedral : 10.230 81.253 4750 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (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 TRP 0.027 0.002 TRP C 112 HIS 0.009 0.001 HIS B 98 PHE 0.027 0.002 PHE B 92 TYR 0.025 0.002 TYR C 33 ARG 0.010 0.001 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.17703 ( 1) link_NAG-ASN : angle 36.68725 ( 3) hydrogen bonds : bond 0.12804 ( 700) hydrogen bonds : angle 7.03471 ( 2028) SS BOND : bond 0.00981 ( 6) SS BOND : angle 2.05716 ( 12) covalent geometry : bond 0.00505 (12962) covalent geometry : angle 0.80816 (17547) *********************** 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 : 1.415 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8666 (mmt) cc_final: 0.8079 (mmt) REVERT: A 104 MET cc_start: 0.7078 (tmm) cc_final: 0.6833 (tmm) REVERT: A 742 ASP cc_start: 0.8908 (p0) cc_final: 0.8561 (p0) REVERT: A 802 TRP cc_start: 0.8825 (t60) cc_final: 0.8243 (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: 0.7991 (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: 0.6266 (m) REVERT: B 154 TRP cc_start: 0.7618 (m100) cc_final: 0.7354 (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: 0.2883 time to fit residues: 98.6420 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 : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.0070 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 356 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 611 HIS A 628 GLN A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.189223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167723 restraints weight = 21153.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164248 restraints weight = 22409.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163921 restraints weight = 26357.667| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12969 Z= 0.141 Angle : 0.663 13.076 17562 Z= 0.348 Chirality : 0.044 0.187 2008 Planarity : 0.005 0.085 2218 Dihedral : 7.145 62.407 1854 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 0.15 % Allowed : 3.81 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1618 helix: 0.10 (0.19), residues: 750 sheet: -0.76 (0.30), residues: 277 loop : -2.31 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 112 HIS 0.009 0.001 HIS B 98 PHE 0.022 0.002 PHE A 758 TYR 0.021 0.002 TYR C 33 ARG 0.010 0.001 ARG A1187 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 1) link_NAG-ASN : angle 3.68674 ( 3) hydrogen bonds : bond 0.05527 ( 700) hydrogen bonds : angle 5.12097 ( 2028) SS BOND : bond 0.00587 ( 6) SS BOND : angle 0.97204 ( 12) covalent geometry : bond 0.00279 (12962) covalent geometry : angle 0.66129 (17547) *********************** 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 193 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.6714 (tmm) cc_final: 0.6443 (tmm) REVERT: A 234 ILE cc_start: 0.7475 (mt) cc_final: 0.7256 (mt) REVERT: A 489 TYR cc_start: 0.7227 (m-80) cc_final: 0.6891 (m-10) REVERT: A 802 TRP cc_start: 0.8868 (t60) cc_final: 0.8516 (t60) REVERT: A 887 LYS cc_start: 0.6666 (mmpt) cc_final: 0.6436 (tptp) REVERT: A 936 VAL cc_start: 0.8105 (p) cc_final: 0.7901 (t) REVERT: B 1 GLN cc_start: 0.7840 (mp10) cc_final: 0.7630 (mp10) REVERT: B 185 LEU cc_start: 0.7022 (mp) cc_final: 0.6804 (mt) REVERT: B 201 GLU cc_start: 0.6219 (mt-10) cc_final: 0.5936 (mt-10) REVERT: C 85 SER cc_start: 0.8296 (m) cc_final: 0.8068 (t) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.2223 time to fit residues: 64.7087 Evaluate side-chains 133 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158970 restraints weight = 20819.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155040 restraints weight = 28743.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.156366 restraints weight = 29243.214| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12969 Z= 0.166 Angle : 0.667 13.302 17562 Z= 0.352 Chirality : 0.045 0.175 2008 Planarity : 0.005 0.084 2218 Dihedral : 6.687 55.425 1854 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1618 helix: 0.51 (0.19), residues: 755 sheet: -0.47 (0.30), residues: 281 loop : -1.94 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 154 HIS 0.009 0.001 HIS B 98 PHE 0.025 0.002 PHE B 92 TYR 0.017 0.002 TYR C 33 ARG 0.004 0.001 ARG A 441 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 3.96046 ( 3) hydrogen bonds : bond 0.05682 ( 700) hydrogen bonds : angle 4.90350 ( 2028) SS BOND : bond 0.00681 ( 6) SS BOND : angle 1.30439 ( 12) covalent geometry : bond 0.00357 (12962) covalent geometry : angle 0.66453 (17547) *********************** 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 194 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8819 (mmm) cc_final: 0.8594 (mmm) REVERT: A 74 MET cc_start: 0.8425 (tmm) cc_final: 0.7792 (tmm) REVERT: A 104 MET cc_start: 0.6821 (tmm) cc_final: 0.6208 (tmm) REVERT: A 297 SER cc_start: 0.8117 (m) cc_final: 0.7384 (p) REVERT: A 947 MET cc_start: 0.8063 (tmm) cc_final: 0.7661 (tpp) REVERT: A 1164 TYR cc_start: 0.8248 (m-80) cc_final: 0.7994 (m-10) REVERT: B 154 TRP cc_start: 0.8429 (m100) cc_final: 0.7295 (m100) REVERT: C 85 SER cc_start: 0.8209 (m) cc_final: 0.7980 (t) REVERT: C 205 ASN cc_start: 0.7527 (m110) cc_final: 0.6768 (m-40) outliers start: 2 outliers final: 0 residues processed: 194 average time/residue: 0.2324 time to fit residues: 67.1279 Evaluate side-chains 137 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 68 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN ** B 98 HIS ** 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 = 0.4005 r_free = 0.4005 target = 0.171887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158235 restraints weight = 19586.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154667 restraints weight = 33357.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152145 restraints weight = 32958.428| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12969 Z= 0.134 Angle : 0.622 13.245 17562 Z= 0.325 Chirality : 0.043 0.172 2008 Planarity : 0.005 0.085 2218 Dihedral : 6.330 53.949 1854 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1618 helix: 0.86 (0.19), residues: 758 sheet: -0.11 (0.31), residues: 274 loop : -1.82 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.005 0.001 HIS A 586 PHE 0.022 0.002 PHE A 956 TYR 0.019 0.001 TYR A 952 ARG 0.007 0.001 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 1) link_NAG-ASN : angle 3.69078 ( 3) hydrogen bonds : bond 0.05156 ( 700) hydrogen bonds : angle 4.62102 ( 2028) SS BOND : bond 0.00425 ( 6) SS BOND : angle 0.96570 ( 12) covalent geometry : bond 0.00279 (12962) covalent geometry : angle 0.62026 (17547) *********************** 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 188 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8512 (tpp) cc_final: 0.8289 (tpp) REVERT: A 50 MET cc_start: 0.8737 (mtt) cc_final: 0.8484 (mmm) REVERT: A 74 MET cc_start: 0.8276 (tmm) cc_final: 0.7849 (tmm) REVERT: A 116 TYR cc_start: 0.7460 (m-10) cc_final: 0.7254 (m-80) REVERT: A 311 LEU cc_start: 0.5097 (mp) cc_final: 0.4887 (tt) REVERT: A 450 VAL cc_start: 0.8098 (t) cc_final: 0.7479 (m) REVERT: A 802 TRP cc_start: 0.8817 (t60) cc_final: 0.8204 (t60) REVERT: A 947 MET cc_start: 0.7840 (tmm) cc_final: 0.7125 (tpp) REVERT: B 86 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 154 TRP cc_start: 0.8143 (m100) cc_final: 0.7239 (m100) REVERT: C 60 TYR cc_start: 0.8428 (m-80) cc_final: 0.8146 (m-80) REVERT: C 85 SER cc_start: 0.8079 (m) cc_final: 0.7803 (t) REVERT: C 205 ASN cc_start: 0.7459 (m110) cc_final: 0.6976 (m-40) REVERT: C 206 VAL cc_start: 0.8847 (t) cc_final: 0.8629 (t) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2975 time to fit residues: 84.6567 Evaluate side-chains 145 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 171 ASN A 586 HIS A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154278 restraints weight = 19699.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151961 restraints weight = 33167.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152153 restraints weight = 32835.782| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12969 Z= 0.132 Angle : 0.614 11.205 17562 Z= 0.322 Chirality : 0.043 0.174 2008 Planarity : 0.004 0.076 2218 Dihedral : 6.065 51.874 1854 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1618 helix: 1.02 (0.19), residues: 752 sheet: 0.13 (0.31), residues: 268 loop : -1.76 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 154 HIS 0.006 0.001 HIS A 586 PHE 0.026 0.002 PHE A1085 TYR 0.021 0.001 TYR A 309 ARG 0.005 0.000 ARG A 441 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 3.59602 ( 3) hydrogen bonds : bond 0.05108 ( 700) hydrogen bonds : angle 4.51245 ( 2028) SS BOND : bond 0.00545 ( 6) SS BOND : angle 1.58583 ( 12) covalent geometry : bond 0.00276 (12962) covalent geometry : angle 0.61059 (17547) *********************** 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 188 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.5971 (mpp80) cc_final: 0.4957 (ttp80) REVERT: A 802 TRP cc_start: 0.8862 (t60) cc_final: 0.8344 (t60) REVERT: A 947 MET cc_start: 0.7729 (tmm) cc_final: 0.7077 (tpp) REVERT: A 1156 PHE cc_start: 0.6915 (t80) cc_final: 0.5514 (m-80) REVERT: A 1183 ILE cc_start: 0.7042 (mt) cc_final: 0.6799 (mm) REVERT: B 86 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8566 (tm-30) REVERT: B 154 TRP cc_start: 0.8341 (m100) cc_final: 0.7435 (m100) REVERT: C 205 ASN cc_start: 0.7395 (m110) cc_final: 0.6825 (m-40) REVERT: C 206 VAL cc_start: 0.8870 (t) cc_final: 0.8620 (t) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2913 time to fit residues: 83.6189 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 : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 35 optimal weight: 4.9990 chunk 80 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153541 restraints weight = 19951.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151147 restraints weight = 35568.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152004 restraints weight = 35150.030| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12969 Z= 0.130 Angle : 0.622 11.815 17562 Z= 0.325 Chirality : 0.044 0.229 2008 Planarity : 0.004 0.070 2218 Dihedral : 5.971 49.430 1854 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1618 helix: 1.10 (0.19), residues: 762 sheet: 0.11 (0.31), residues: 276 loop : -1.66 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.006 0.001 HIS A 586 PHE 0.020 0.001 PHE B 92 TYR 0.022 0.001 TYR A 309 ARG 0.004 0.000 ARG A1046 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 1) link_NAG-ASN : angle 3.52941 ( 3) hydrogen bonds : bond 0.04961 ( 700) hydrogen bonds : angle 4.45490 ( 2028) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.14883 ( 12) covalent geometry : bond 0.00267 (12962) covalent geometry : angle 0.61943 (17547) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7494 (m) cc_final: 0.7086 (t) REVERT: A 802 TRP cc_start: 0.8899 (t60) cc_final: 0.8324 (t60) REVERT: A 947 MET cc_start: 0.7670 (tmm) cc_final: 0.7016 (tpp) REVERT: A 1156 PHE cc_start: 0.7255 (t80) cc_final: 0.5625 (m-80) REVERT: B 86 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 140 CYS cc_start: 0.6650 (m) cc_final: 0.6080 (m) REVERT: B 154 TRP cc_start: 0.8383 (m100) cc_final: 0.7345 (m100) REVERT: C 205 ASN cc_start: 0.7483 (m110) cc_final: 0.6819 (m-40) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2171 time to fit residues: 60.1101 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 : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155986 restraints weight = 19480.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153660 restraints weight = 30079.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153302 restraints weight = 32160.031| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12969 Z= 0.125 Angle : 0.612 11.528 17562 Z= 0.320 Chirality : 0.043 0.211 2008 Planarity : 0.004 0.071 2218 Dihedral : 5.890 48.756 1854 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1618 helix: 1.19 (0.19), residues: 762 sheet: 0.35 (0.32), residues: 267 loop : -1.71 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 154 HIS 0.008 0.001 HIS B 98 PHE 0.019 0.001 PHE B 92 TYR 0.021 0.001 TYR A 309 ARG 0.003 0.000 ARG A1046 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 3.17778 ( 3) hydrogen bonds : bond 0.04872 ( 700) hydrogen bonds : angle 4.39460 ( 2028) SS BOND : bond 0.00475 ( 6) SS BOND : angle 1.27754 ( 12) covalent geometry : bond 0.00253 (12962) covalent geometry : angle 0.60991 (17547) *********************** 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 183 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7124 (m) cc_final: 0.6725 (t) REVERT: A 802 TRP cc_start: 0.8914 (t60) cc_final: 0.8358 (t60) REVERT: A 947 MET cc_start: 0.7397 (tmm) cc_final: 0.6841 (tpp) REVERT: B 185 LEU cc_start: 0.7049 (mp) cc_final: 0.6849 (mp) REVERT: C 205 ASN cc_start: 0.7419 (m110) cc_final: 0.6567 (m-40) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2412 time to fit residues: 68.5655 Evaluate side-chains 131 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 160 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3893 r_free = 0.3893 target = 0.161635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147424 restraints weight = 19972.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.142249 restraints weight = 36533.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141055 restraints weight = 32818.019| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12969 Z= 0.168 Angle : 0.688 12.297 17562 Z= 0.363 Chirality : 0.046 0.198 2008 Planarity : 0.005 0.077 2218 Dihedral : 6.064 48.060 1854 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1618 helix: 0.99 (0.19), residues: 761 sheet: -0.05 (0.30), residues: 287 loop : -1.60 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 231 HIS 0.009 0.001 HIS B 98 PHE 0.028 0.002 PHE B 92 TYR 0.033 0.002 TYR A 306 ARG 0.005 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 1) link_NAG-ASN : angle 3.01189 ( 3) hydrogen bonds : bond 0.05648 ( 700) hydrogen bonds : angle 4.65255 ( 2028) SS BOND : bond 0.00530 ( 6) SS BOND : angle 1.25586 ( 12) covalent geometry : bond 0.00374 (12962) covalent geometry : angle 0.68665 (17547) *********************** 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 171 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8436 (tmm) cc_final: 0.7970 (tmm) REVERT: A 450 VAL cc_start: 0.8737 (t) cc_final: 0.8529 (m) REVERT: A 513 MET cc_start: 0.3973 (tmm) cc_final: 0.3720 (tmm) REVERT: A 802 TRP cc_start: 0.8996 (t60) cc_final: 0.8452 (t60) REVERT: A 947 MET cc_start: 0.7592 (tmm) cc_final: 0.7026 (tpp) REVERT: A 1055 LEU cc_start: 0.7299 (tp) cc_final: 0.7063 (tt) REVERT: B 154 TRP cc_start: 0.8485 (m100) cc_final: 0.7675 (m100) REVERT: C 205 ASN cc_start: 0.7463 (m110) cc_final: 0.6954 (m-40) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2647 time to fit residues: 70.9388 Evaluate side-chains 122 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.173446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158554 restraints weight = 21029.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156140 restraints weight = 36999.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156707 restraints weight = 35282.235| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12969 Z= 0.135 Angle : 0.640 12.143 17562 Z= 0.334 Chirality : 0.044 0.204 2008 Planarity : 0.004 0.068 2218 Dihedral : 5.961 49.004 1854 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1618 helix: 1.13 (0.19), residues: 760 sheet: 0.06 (0.31), residues: 284 loop : -1.54 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 154 HIS 0.004 0.001 HIS B 98 PHE 0.029 0.002 PHE A 207 TYR 0.021 0.001 TYR A 927 ARG 0.003 0.000 ARG A1046 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 1) link_NAG-ASN : angle 2.82079 ( 3) hydrogen bonds : bond 0.05223 ( 700) hydrogen bonds : angle 4.48857 ( 2028) SS BOND : bond 0.00400 ( 6) SS BOND : angle 1.38378 ( 12) covalent geometry : bond 0.00282 (12962) covalent geometry : angle 0.63857 (17547) *********************** 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 172 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.8015 (m) cc_final: 0.7394 (p) REVERT: A 518 GLN cc_start: 0.7442 (mt0) cc_final: 0.6668 (mp10) REVERT: A 802 TRP cc_start: 0.8952 (t60) cc_final: 0.8400 (t60) REVERT: A 947 MET cc_start: 0.7391 (tmm) cc_final: 0.6885 (tpp) REVERT: A 1055 LEU cc_start: 0.7222 (tp) cc_final: 0.6933 (tt) REVERT: B 154 TRP cc_start: 0.8387 (m100) cc_final: 0.7520 (m100) REVERT: C 205 ASN cc_start: 0.7510 (m110) cc_final: 0.6866 (m-40) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2366 time to fit residues: 62.7243 Evaluate side-chains 124 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 145 optimal weight: 0.0070 chunk 126 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 GLN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.174462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.161020 restraints weight = 20992.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156924 restraints weight = 39319.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154823 restraints weight = 32963.511| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5817 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= 0.125 Angle : 0.619 12.355 17562 Z= 0.322 Chirality : 0.043 0.204 2008 Planarity : 0.004 0.068 2218 Dihedral : 5.871 50.361 1854 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1618 helix: 1.19 (0.19), residues: 766 sheet: 0.14 (0.31), residues: 291 loop : -1.54 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 154 HIS 0.004 0.001 HIS B 98 PHE 0.025 0.001 PHE A 207 TYR 0.022 0.001 TYR A 927 ARG 0.002 0.000 ARG A1046 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 2.67849 ( 3) hydrogen bonds : bond 0.04907 ( 700) hydrogen bonds : angle 4.36049 ( 2028) SS BOND : bond 0.00411 ( 6) SS BOND : angle 1.10372 ( 12) covalent geometry : bond 0.00254 (12962) covalent geometry : angle 0.61771 (17547) ********************** 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 181 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 518 GLN cc_start: 0.7220 (mt0) cc_final: 0.6517 (mp10) REVERT: A 802 TRP cc_start: 0.8924 (t60) cc_final: 0.8446 (t60) REVERT: A 947 MET cc_start: 0.7407 (tmm) cc_final: 0.6903 (tpp) REVERT: B 185 LEU cc_start: 0.6852 (mp) cc_final: 0.6647 (mp) REVERT: C 205 ASN cc_start: 0.7420 (m110) cc_final: 0.6571 (m-40) REVERT: C 206 VAL cc_start: 0.9063 (t) cc_final: 0.8771 (p) REVERT: C 216 ASP cc_start: 0.8274 (m-30) cc_final: 0.8067 (m-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2512 time to fit residues: 70.4701 Evaluate side-chains 131 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 109 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4053 r_free = 0.4053 target = 0.173974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160527 restraints weight = 20950.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156407 restraints weight = 37716.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155058 restraints weight = 35260.201| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12969 Z= 0.125 Angle : 0.627 12.138 17562 Z= 0.325 Chirality : 0.043 0.236 2008 Planarity : 0.004 0.066 2218 Dihedral : 5.837 51.126 1854 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1618 helix: 1.24 (0.19), residues: 765 sheet: 0.19 (0.31), residues: 287 loop : -1.49 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 707 HIS 0.004 0.001 HIS B 98 PHE 0.024 0.001 PHE A 207 TYR 0.040 0.001 TYR A 246 ARG 0.003 0.000 ARG A1046 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 2.62238 ( 3) hydrogen bonds : bond 0.04836 ( 700) hydrogen bonds : angle 4.33996 ( 2028) SS BOND : bond 0.00420 ( 6) SS BOND : angle 1.04718 ( 12) covalent geometry : bond 0.00257 (12962) covalent geometry : angle 0.62551 (17547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.67 seconds wall clock time: 73 minutes 50.02 seconds (4430.02 seconds total)