Starting phenix.real_space_refine on Fri Aug 7 00:32:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1q_61978/08_2026/9k1q_61978.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1q_61978/08_2026/9k1q_61978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1q_61978/08_2026/9k1q_61978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1q_61978/08_2026/9k1q_61978.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1q_61978/08_2026/9k1q_61978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1q_61978/08_2026/9k1q_61978.cif" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 31 5.49 5 S 102 5.16 5 C 11141 2.51 5 N 3043 2.21 5 O 3370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17690 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 6478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6478 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 34, 'TRANS': 779} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9158 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 60, 'TRANS': 1107} Chain breaks: 5 Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 584 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 461 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 12} Chain: "H" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6647 SG CYS D 23 97.713 53.125 42.746 1.00 38.71 S ATOM 6671 SG CYS D 26 95.987 49.939 43.780 1.00 43.30 S ATOM 6918 SG CYS D 58 96.969 52.569 46.422 1.00 30.83 S ATOM 6939 SG CYS D 61 99.667 50.574 44.768 1.00 31.77 S ATOM 6560 SG CYS D 11 97.024 48.354 60.872 1.00 28.40 S ATOM 6823 SG CYS D 46 97.352 52.094 61.917 1.00 27.88 S ATOM 6846 SG CYS D 49 98.900 50.936 58.741 1.00 32.87 S ATOM 7117 SG CYS D 85 95.079 51.020 59.082 1.00 26.83 S ATOM 6698 SG CYS D 30 85.777 46.928 49.038 1.00 33.05 S ATOM 6719 SG CYS D 33 84.700 43.435 48.017 1.00 35.40 S ATOM 7014 SG CYS D 72 82.069 45.997 48.790 1.00 21.43 S ATOM 7038 SG CYS D 75 84.011 44.643 51.622 1.00 19.93 S Time building chain proxies: 3.25, per 1000 atoms: 0.18 Number of scatterers: 17690 At special positions: 0 Unit cell: (146.3, 117.7, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 102 16.00 P 31 15.00 O 3370 8.00 N 3043 7.00 C 11141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 474.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 26 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " Number of angles added : 18 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4040 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 28 sheets defined 41.5% alpha, 18.2% beta 5 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'C' and resid 491 through 496 Processing helix chain 'C' and resid 496 through 506 removed outlier: 4.062A pdb=" N LEU C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 527 removed outlier: 5.076A pdb=" N ARG C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU C 525 " --> pdb=" O ASP C 521 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 541 Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 563 Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 584 Proline residue: C 580 - end of helix removed outlier: 3.695A pdb=" N ASP C 584 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 604 Processing helix chain 'C' and resid 605 through 614 removed outlier: 3.588A pdb=" N MET C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 619 removed outlier: 4.132A pdb=" N ASP C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 619 " --> pdb=" O ASP C 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 619' Processing helix chain 'C' and resid 621 through 638 removed outlier: 3.625A pdb=" N ARG C 625 " --> pdb=" O ASP C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 657 through 676 removed outlier: 4.059A pdb=" N ARG C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY C 676 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 682 through 696 removed outlier: 3.745A pdb=" N LEU C 686 " --> pdb=" O HIS C 682 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 716 Processing helix chain 'C' and resid 727 through 738 removed outlier: 3.503A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 778 removed outlier: 4.378A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLN C 778 " --> pdb=" O ILE C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 798 Processing helix chain 'C' and resid 802 through 810 Processing helix chain 'C' and resid 810 through 818 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 827 through 845 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 855 through 859 Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 885 through 902 Processing helix chain 'C' and resid 908 through 922 Processing helix chain 'C' and resid 923 through 927 Proline residue: C 927 - end of helix Processing helix chain 'C' and resid 928 through 941 Processing helix chain 'C' and resid 947 through 965 removed outlier: 4.942A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.727A pdb=" N ILE C1004 " --> pdb=" O ILE C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1009 Processing helix chain 'C' and resid 1012 through 1025 Proline residue: C1018 - end of helix Proline residue: C1022 - end of helix Processing helix chain 'C' and resid 1028 through 1045 Processing helix chain 'C' and resid 1051 through 1066 Processing helix chain 'C' and resid 1070 through 1088 Processing helix chain 'C' and resid 1091 through 1099 Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 3.506A pdb=" N ARG C1109 " --> pdb=" O GLU C1105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS C1111 " --> pdb=" O GLN C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1137 Processing helix chain 'C' and resid 1140 through 1159 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.552A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C1164 " --> pdb=" O MET C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 3.779A pdb=" N VAL C1169 " --> pdb=" O TYR C1165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C1170 " --> pdb=" O ILE C1166 " (cutoff:3.500A) Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1181 through 1199 Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.580A pdb=" N LEU C1208 " --> pdb=" O CYS C1204 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C1210 " --> pdb=" O ASP C1206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1219 No H-bonds generated for 'chain 'C' and resid 1217 through 1219' Processing helix chain 'C' and resid 1223 through 1242 Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.848A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1259 through 1275 removed outlier: 3.917A pdb=" N GLY C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1278 No H-bonds generated for 'chain 'C' and resid 1276 through 1278' Processing helix chain 'C' and resid 1279 through 1284 Processing helix chain 'C' and resid 1297 through 1302 removed outlier: 3.868A pdb=" N TYR C1302 " --> pdb=" O GLU C1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.692A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.911A pdb=" N CYS A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 removed outlier: 3.858A pdb=" N ALA A 827 " --> pdb=" O MET A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 removed outlier: 4.478A pdb=" N ALA A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.964A pdb=" N GLY A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 935' Processing helix chain 'A' and resid 1134 through 1152 Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1176 through 1182 Processing helix chain 'A' and resid 1183 through 1185 No H-bonds generated for 'chain 'A' and resid 1183 through 1185' Processing helix chain 'A' and resid 1186 through 1197 removed outlier: 3.680A pdb=" N GLN A1190 " --> pdb=" O GLU A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.772A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.581A pdb=" N TRP B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 60 through 72 Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.581A pdb=" N THR D 41 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1129 through 1131 Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.559A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 32 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 39 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG A 42 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR A 52 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.515A pdb=" N SER A 64 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 80 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 89 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 103 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.639A pdb=" N MET A 98 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 123 removed outlier: 3.554A pdb=" N ASN A 145 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 173 removed outlier: 3.671A pdb=" N TYR A 168 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 185 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 170 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA A 183 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLY A 172 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET A 181 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 232 through 238 removed outlier: 6.850A pdb=" N CYS A 251 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 235 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 249 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR A 237 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 247 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 267 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.162A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 293 removed outlier: 3.967A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 287 through 293 removed outlier: 3.967A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 331 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.771A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.559A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 449 through 450 removed outlier: 3.606A pdb=" N SER A 450 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.087A pdb=" N ALA A 458 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 477 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 485 through 486 removed outlier: 3.737A pdb=" N SER A 486 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 492 " --> pdb=" O SER A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.789A pdb=" N TYR A 520 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.628A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 590 through 592 removed outlier: 4.036A pdb=" N ALA A 606 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 637 through 643 Processing sheet with id=AC4, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.626A pdb=" N PHE A 702 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 704 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 711 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 724 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 722 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.324A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 866 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 879 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 868 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 886 through 894 removed outlier: 9.063A pdb=" N GLU A 886 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP A 912 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA A 888 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 910 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 890 " --> pdb=" O GLY A 908 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 907 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 913 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL A 920 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 927 " --> pdb=" O HIS A 941 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS A 941 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 949 through 955 removed outlier: 6.631A pdb=" N GLY A 962 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 952 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 960 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG A 958 " --> pdb=" O PRO A 954 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 969 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 990 through 996 removed outlier: 3.955A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A1087 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A1026 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 6.732A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A1090 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1101 through 1106 755 hydrogen bonds defined for protein. 2154 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3786 1.33 - 1.45: 3979 1.45 - 1.57: 10119 1.57 - 1.69: 60 1.69 - 1.81: 157 Bond restraints: 18101 Sorted by residual: bond pdb=" N9 G G 45 " pdb=" C4 G G 45 " ideal model delta sigma weight residual 1.375 1.389 -0.014 8.00e-03 1.56e+04 3.14e+00 bond pdb=" N9 A H 26 " pdb=" C4 A H 26 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.59e+00 bond pdb=" C8 G H 28 " pdb=" N7 G H 28 " ideal model delta sigma weight residual 1.305 1.298 0.007 6.00e-03 2.78e+04 1.55e+00 bond pdb=" C THR C 717 " pdb=" N PRO C 718 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.49e+00 bond pdb=" N9 A H 29 " pdb=" C4 A H 29 " ideal model delta sigma weight residual 1.374 1.381 -0.007 6.00e-03 2.78e+04 1.43e+00 ... (remaining 18096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 24209 1.64 - 3.28: 376 3.28 - 4.93: 54 4.93 - 6.57: 20 6.57 - 8.21: 5 Bond angle restraints: 24664 Sorted by residual: angle pdb=" O5' G G 45 " pdb=" C5' G G 45 " pdb=" C4' G G 45 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.82e+01 angle pdb=" N GLU A1195 " pdb=" CA GLU A1195 " pdb=" CB GLU A1195 " ideal model delta sigma weight residual 110.28 116.21 -5.93 1.55e+00 4.16e-01 1.46e+01 angle pdb=" C TYR C 979 " pdb=" N GLU C 980 " pdb=" CA GLU C 980 " ideal model delta sigma weight residual 121.18 113.62 7.56 1.98e+00 2.55e-01 1.46e+01 angle pdb=" O5' G H 28 " pdb=" C5' G H 28 " pdb=" C4' G H 28 " ideal model delta sigma weight residual 109.40 112.40 -3.00 8.00e-01 1.56e+00 1.41e+01 angle pdb=" C3' G G 45 " pdb=" O3' G G 45 " pdb=" P C G 46 " ideal model delta sigma weight residual 119.70 124.14 -4.44 1.20e+00 6.94e-01 1.37e+01 ... (remaining 24659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 10708 34.84 - 69.69: 276 69.69 - 104.53: 38 104.53 - 139.38: 0 139.38 - 174.22: 1 Dihedral angle restraints: 11023 sinusoidal: 4751 harmonic: 6272 Sorted by residual: dihedral pdb=" O4' C G 44 " pdb=" C1' C G 44 " pdb=" N1 C G 44 " pdb=" C2 C G 44 " ideal model delta sinusoidal sigma weight residual 232.00 57.78 174.22 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA LYS C 943 " pdb=" C LYS C 943 " pdb=" N SER C 944 " pdb=" CA SER C 944 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER C 944 " pdb=" C SER C 944 " pdb=" N ALA C 945 " pdb=" CA ALA C 945 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 11020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2053 0.037 - 0.074: 475 0.074 - 0.112: 224 0.112 - 0.149: 70 0.149 - 0.186: 3 Chirality restraints: 2825 Sorted by residual: chirality pdb=" CA GLN C 518 " pdb=" N GLN C 518 " pdb=" C GLN C 518 " pdb=" CB GLN C 518 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA LYS C 943 " pdb=" N LYS C 943 " pdb=" C LYS C 943 " pdb=" CB LYS C 943 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA THR C1010 " pdb=" N THR C1010 " pdb=" C THR C1010 " pdb=" CB THR C1010 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2822 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 926 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO C 927 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 927 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 927 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1083 " 0.012 2.00e-02 2.50e+03 1.29e-02 3.35e+00 pdb=" CG TYR C1083 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C1083 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C1083 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C1083 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C1083 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C1083 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C1083 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 508 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO C 509 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 509 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 509 " 0.021 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 802 2.73 - 3.27: 17208 3.27 - 3.81: 28586 3.81 - 4.36: 32594 4.36 - 4.90: 57685 Nonbonded interactions: 136875 Sorted by model distance: nonbonded pdb=" O LYS A1191 " pdb=" OG SER A1194 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR B 27 " pdb=" OE1 GLU B 30 " model vdw 2.204 3.040 nonbonded pdb=" O GLU A 186 " pdb=" OG1 THR A 207 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 136 " pdb=" OH TYR A 189 " model vdw 2.244 3.040 nonbonded pdb=" NE2 HIS C 550 " pdb=" OD1 ASP D 97 " model vdw 2.250 3.120 ... (remaining 136870 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: 1.220 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.002 0.035 18113 Z= 0.104 Angle : 0.521 8.212 24682 Z= 0.297 Chirality : 0.042 0.186 2825 Planarity : 0.003 0.068 3067 Dihedral : 15.913 174.220 6983 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.19), residues: 2140 helix: 1.48 (0.20), residues: 801 sheet: 0.69 (0.28), residues: 426 loop : -1.09 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 517 TYR 0.032 0.001 TYR C1083 PHE 0.022 0.001 PHE C1081 TRP 0.008 0.000 TRP C1055 HIS 0.003 0.000 HIS C 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 (18101) covalent geometry : angle 0.51782 / 0.30 (24664) hydrogen bonds : bond 0.16964 / 11.03 ( 759) hydrogen bonds : angle 7.24119 / 5.43 ( 2180) metal coordination : bond 0.00256 / 0.17 ( 12) metal coordination : angle 2.33994 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 671 ILE cc_start: 0.8103 (mm) cc_final: 0.7765 (mm) REVERT: C 878 ASN cc_start: 0.7194 (m-40) cc_final: 0.6971 (m-40) REVERT: A 447 MET cc_start: 0.0396 (ptt) cc_final: -0.0316 (ttp) REVERT: A 706 MET cc_start: 0.3022 (tpt) cc_final: 0.2769 (tpt) REVERT: A 945 VAL cc_start: 0.6445 (t) cc_final: 0.6229 (t) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1039 time to fit residues: 39.2193 Evaluate side-chains 177 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN C 669 GLN C 670 GLN C1007 HIS C1100 ASN C1107 GLN C1277 GLN A 796 ASN A 941 HIS A1138 HIS B 23 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115881 restraints weight = 33861.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115680 restraints weight = 28091.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115965 restraints weight = 25088.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118266 restraints weight = 20556.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117772 restraints weight = 16717.771| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18113 Z= 0.249 Angle : 0.699 10.526 24682 Z= 0.358 Chirality : 0.047 0.203 2825 Planarity : 0.006 0.093 3067 Dihedral : 12.749 176.055 2832 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.29 % Allowed : 9.12 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.22 (0.18), residues: 2140 helix: 1.18 (0.19), residues: 793 sheet: 0.01 (0.26), residues: 422 loop : -1.40 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 827 TYR 0.021 0.002 TYR A 4 PHE 0.025 0.002 PHE A 955 TRP 0.012 0.002 TRP B 29 HIS 0.012 0.002 HIS C1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (18101) covalent geometry : angle 0.68550 / 0.36 (24664) hydrogen bonds : bond 0.05391 / 3.53 ( 759) hydrogen bonds : angle 5.49278 / 4.11 ( 2180) metal coordination : bond 0.01051 / 0.65 ( 12) metal coordination : angle 5.09767 / 2.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1121 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7910 (tm-30) REVERT: D 55 GLN cc_start: 0.6749 (tt0) cc_final: 0.6368 (tm-30) REVERT: A 447 MET cc_start: 0.0490 (ptt) cc_final: -0.0169 (ttp) REVERT: A 706 MET cc_start: 0.3272 (tpt) cc_final: 0.2830 (tpt) REVERT: B 59 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6647 (mm-30) outliers start: 24 outliers final: 16 residues processed: 197 average time/residue: 0.1105 time to fit residues: 34.1813 Evaluate side-chains 175 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 550 HIS Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 26 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 187 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 139 optimal weight: 0.0870 chunk 170 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 164 optimal weight: 0.0370 chunk 163 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 534 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.152153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119652 restraints weight = 33937.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120081 restraints weight = 29386.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120744 restraints weight = 23372.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121251 restraints weight = 18506.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121465 restraints weight = 16642.488| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18113 Z= 0.104 Angle : 0.538 7.672 24682 Z= 0.274 Chirality : 0.042 0.183 2825 Planarity : 0.004 0.048 3067 Dihedral : 12.625 175.527 2832 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.97 % Allowed : 10.94 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.03 (0.19), residues: 2140 helix: 1.40 (0.19), residues: 801 sheet: 0.13 (0.26), residues: 425 loop : -1.39 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 614 TYR 0.014 0.001 TYR C 830 PHE 0.020 0.001 PHE A 261 TRP 0.008 0.001 TRP B 29 HIS 0.004 0.001 HIS A 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (18101) covalent geometry : angle 0.53081 / 0.27 (24664) hydrogen bonds : bond 0.03967 / 2.58 ( 759) hydrogen bonds : angle 5.07657 / 3.81 ( 2180) metal coordination : bond 0.00348 / 0.23 ( 12) metal coordination : angle 3.34276 / 1.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7252 (mmm) cc_final: 0.6723 (mtp) REVERT: C 1113 THR cc_start: 0.8674 (m) cc_final: 0.8444 (p) REVERT: D 55 GLN cc_start: 0.6716 (tt0) cc_final: 0.6336 (tm-30) REVERT: D 73 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8028 (tptp) REVERT: A 181 MET cc_start: 0.8233 (mmm) cc_final: 0.7951 (tpp) REVERT: A 298 MET cc_start: 0.6979 (ttt) cc_final: 0.6712 (ttt) REVERT: A 447 MET cc_start: 0.0323 (ptt) cc_final: -0.0254 (ttp) REVERT: A 706 MET cc_start: 0.3257 (tpt) cc_final: 0.2848 (tpt) REVERT: B 59 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6618 (mm-30) outliers start: 18 outliers final: 12 residues processed: 207 average time/residue: 0.1009 time to fit residues: 33.2657 Evaluate side-chains 173 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 141 optimal weight: 0.4980 chunk 163 optimal weight: 0.0170 chunk 25 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.152864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120891 restraints weight = 33784.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121154 restraints weight = 29715.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121904 restraints weight = 22800.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122214 restraints weight = 18997.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122278 restraints weight = 17502.775| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18113 Z= 0.098 Angle : 0.522 8.199 24682 Z= 0.266 Chirality : 0.042 0.232 2825 Planarity : 0.004 0.044 3067 Dihedral : 12.557 175.392 2832 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.39 % Allowed : 11.80 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.06 (0.19), residues: 2140 helix: 1.43 (0.19), residues: 802 sheet: 0.26 (0.26), residues: 422 loop : -1.35 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 827 TYR 0.017 0.001 TYR A 258 PHE 0.024 0.001 PHE A 261 TRP 0.008 0.001 TRP C1055 HIS 0.003 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (18101) covalent geometry : angle 0.51622 / 0.27 (24664) hydrogen bonds : bond 0.03444 / 2.24 ( 759) hydrogen bonds : angle 4.82341 / 3.61 ( 2180) metal coordination : bond 0.00293 / 0.19 ( 12) metal coordination : angle 2.88273 / 1.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7223 (mmm) cc_final: 0.6646 (mtp) REVERT: C 655 LYS cc_start: 0.7853 (tptp) cc_final: 0.7580 (tptm) REVERT: D 55 GLN cc_start: 0.6643 (tt0) cc_final: 0.6310 (tm-30) REVERT: D 73 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8022 (tptp) REVERT: A 181 MET cc_start: 0.8193 (mmm) cc_final: 0.7981 (tpp) REVERT: A 315 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 447 MET cc_start: 0.0236 (ptt) cc_final: -0.0322 (ttp) REVERT: A 706 MET cc_start: 0.3250 (tpt) cc_final: 0.2848 (tpt) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.1022 time to fit residues: 32.1945 Evaluate side-chains 186 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 0.0030 chunk 102 optimal weight: 0.0030 chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 HIS C1100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120766 restraints weight = 33756.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121745 restraints weight = 29830.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122119 restraints weight = 22759.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122555 restraints weight = 17696.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122726 restraints weight = 16298.329| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18113 Z= 0.098 Angle : 0.522 9.209 24682 Z= 0.263 Chirality : 0.042 0.270 2825 Planarity : 0.003 0.042 3067 Dihedral : 12.538 175.891 2832 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.34 % Allowed : 12.82 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.06 (0.19), residues: 2140 helix: 1.44 (0.19), residues: 802 sheet: 0.22 (0.26), residues: 418 loop : -1.33 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 775 TYR 0.010 0.001 TYR A 4 PHE 0.022 0.001 PHE A 261 TRP 0.007 0.001 TRP C1055 HIS 0.008 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (18101) covalent geometry : angle 0.51668 / 0.26 (24664) hydrogen bonds : bond 0.03348 / 2.17 ( 759) hydrogen bonds : angle 4.70745 / 3.52 ( 2180) metal coordination : bond 0.00305 / 0.20 ( 12) metal coordination : angle 2.90559 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7254 (mmm) cc_final: 0.6768 (mtp) REVERT: D 55 GLN cc_start: 0.6680 (tt0) cc_final: 0.6205 (tm-30) REVERT: D 73 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8003 (tptp) REVERT: A 447 MET cc_start: 0.0303 (ptt) cc_final: -0.0266 (ttp) REVERT: A 706 MET cc_start: 0.3295 (tpt) cc_final: 0.2775 (tpt) outliers start: 25 outliers final: 21 residues processed: 195 average time/residue: 0.1098 time to fit residues: 34.4369 Evaluate side-chains 185 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 HIS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 106 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 202 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.152504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120786 restraints weight = 33473.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122288 restraints weight = 28324.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122498 restraints weight = 21582.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122743 restraints weight = 18149.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122796 restraints weight = 16152.347| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18113 Z= 0.098 Angle : 0.519 9.004 24682 Z= 0.262 Chirality : 0.042 0.214 2825 Planarity : 0.003 0.040 3067 Dihedral : 12.527 176.347 2832 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.55 % Allowed : 13.73 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.07 (0.19), residues: 2140 helix: 1.44 (0.19), residues: 803 sheet: 0.22 (0.26), residues: 417 loop : -1.31 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 549 TYR 0.015 0.001 TYR C 979 PHE 0.019 0.001 PHE A 261 TRP 0.007 0.001 TRP C1055 HIS 0.011 0.001 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (18101) covalent geometry : angle 0.51245 / 0.26 (24664) hydrogen bonds : bond 0.03325 / 2.14 ( 759) hydrogen bonds : angle 4.63027 / 3.45 ( 2180) metal coordination : bond 0.00316 / 0.21 ( 12) metal coordination : angle 2.97282 / 1.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7231 (mmm) cc_final: 0.6781 (mtp) REVERT: D 55 GLN cc_start: 0.6654 (tt0) cc_final: 0.6171 (tm-30) REVERT: D 73 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8015 (tptp) REVERT: A 447 MET cc_start: -0.0010 (ptt) cc_final: -0.0524 (ttp) REVERT: A 706 MET cc_start: 0.3315 (tpt) cc_final: 0.2781 (tpt) outliers start: 29 outliers final: 23 residues processed: 188 average time/residue: 0.1091 time to fit residues: 33.0771 Evaluate side-chains 184 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 HIS Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1081 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 102 optimal weight: 0.0020 chunk 197 optimal weight: 0.2980 chunk 155 optimal weight: 0.0070 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.153273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121401 restraints weight = 33712.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122919 restraints weight = 29894.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.123208 restraints weight = 21520.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123732 restraints weight = 16728.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123712 restraints weight = 15844.238| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18113 Z= 0.094 Angle : 0.522 11.096 24682 Z= 0.262 Chirality : 0.042 0.260 2825 Planarity : 0.003 0.038 3067 Dihedral : 12.513 176.572 2832 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.39 % Allowed : 14.37 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.19), residues: 2140 helix: 1.46 (0.19), residues: 807 sheet: 0.28 (0.26), residues: 415 loop : -1.27 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 614 TYR 0.009 0.001 TYR A 224 PHE 0.019 0.001 PHE A 261 TRP 0.008 0.001 TRP C1055 HIS 0.011 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (18101) covalent geometry : angle 0.51682 / 0.26 (24664) hydrogen bonds : bond 0.03124 / 2.02 ( 759) hydrogen bonds : angle 4.55350 / 3.39 ( 2180) metal coordination : bond 0.00288 / 0.18 ( 12) metal coordination : angle 2.77971 / 1.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7213 (mmm) cc_final: 0.6774 (mtp) REVERT: D 55 GLN cc_start: 0.6639 (tt0) cc_final: 0.6149 (tm-30) REVERT: D 73 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8008 (tptp) REVERT: A 447 MET cc_start: -0.0019 (ptt) cc_final: -0.0537 (ttp) REVERT: A 706 MET cc_start: 0.3305 (tpt) cc_final: 0.2772 (tpt) outliers start: 26 outliers final: 21 residues processed: 196 average time/residue: 0.1163 time to fit residues: 36.7029 Evaluate side-chains 186 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 HIS Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 1081 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.153020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.120272 restraints weight = 33642.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120397 restraints weight = 28027.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121303 restraints weight = 20665.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121818 restraints weight = 16950.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121875 restraints weight = 15681.936| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18113 Z= 0.098 Angle : 0.528 8.911 24682 Z= 0.265 Chirality : 0.042 0.289 2825 Planarity : 0.003 0.038 3067 Dihedral : 12.500 177.018 2832 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.34 % Allowed : 14.91 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.13 (0.19), residues: 2140 helix: 1.46 (0.19), residues: 808 sheet: 0.26 (0.26), residues: 415 loop : -1.26 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 614 TYR 0.016 0.001 TYR C 561 PHE 0.017 0.001 PHE A 261 TRP 0.007 0.001 TRP C1055 HIS 0.009 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (18101) covalent geometry : angle 0.52261 / 0.26 (24664) hydrogen bonds : bond 0.03146 / 2.05 ( 759) hydrogen bonds : angle 4.51587 / 3.36 ( 2180) metal coordination : bond 0.00302 / 0.19 ( 12) metal coordination : angle 2.93618 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7398 (mmm) cc_final: 0.6911 (mtp) REVERT: C 823 MET cc_start: 0.3805 (ptm) cc_final: 0.3496 (ttp) REVERT: C 962 MET cc_start: 0.7321 (tpp) cc_final: 0.7118 (tpp) REVERT: D 55 GLN cc_start: 0.6644 (tt0) cc_final: 0.6137 (tm-30) REVERT: D 73 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8011 (tptp) REVERT: A 55 THR cc_start: 0.8006 (m) cc_final: 0.7755 (p) REVERT: A 447 MET cc_start: 0.0088 (ptt) cc_final: -0.0515 (ttp) REVERT: A 706 MET cc_start: 0.3302 (tpt) cc_final: 0.2754 (tpt) outliers start: 25 outliers final: 19 residues processed: 190 average time/residue: 0.1154 time to fit residues: 34.9164 Evaluate side-chains 177 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 HIS Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 1081 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 115 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 HIS D 78 GLN ** A 304 GLN ** 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 = 0.4038 r_free = 0.4038 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115603 restraints weight = 33671.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115973 restraints weight = 28445.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116650 restraints weight = 22426.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117022 restraints weight = 17471.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117021 restraints weight = 16368.349| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18113 Z= 0.191 Angle : 0.633 11.546 24682 Z= 0.321 Chirality : 0.045 0.241 2825 Planarity : 0.004 0.045 3067 Dihedral : 12.698 178.779 2832 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.45 % Allowed : 15.28 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.20 (0.18), residues: 2140 helix: 1.24 (0.19), residues: 805 sheet: -0.19 (0.25), residues: 442 loop : -1.37 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 614 TYR 0.015 0.002 TYR A 4 PHE 0.025 0.002 PHE A 955 TRP 0.013 0.002 TRP C 819 HIS 0.025 0.002 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (18101) covalent geometry : angle 0.62104 / 0.32 (24664) hydrogen bonds : bond 0.04446 / 2.87 ( 759) hydrogen bonds : angle 4.70908 / 3.49 ( 2180) metal coordination : bond 0.00719 / 0.44 ( 12) metal coordination : angle 4.56471 / 2.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 600 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7116 (tt) REVERT: C 823 MET cc_start: 0.3713 (ptm) cc_final: 0.3481 (ttp) REVERT: D 73 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8061 (tptp) REVERT: A 447 MET cc_start: 0.0275 (ptt) cc_final: -0.0404 (ttp) REVERT: A 706 MET cc_start: 0.3360 (tpt) cc_final: 0.2777 (tpt) outliers start: 27 outliers final: 23 residues processed: 180 average time/residue: 0.1188 time to fit residues: 34.5638 Evaluate side-chains 175 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 1081 PHE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.148938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116393 restraints weight = 33506.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117098 restraints weight = 28707.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117662 restraints weight = 22376.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117867 restraints weight = 17754.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118076 restraints weight = 16291.293| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18113 Z= 0.144 Angle : 0.595 9.669 24682 Z= 0.300 Chirality : 0.044 0.267 2825 Planarity : 0.004 0.041 3067 Dihedral : 12.722 178.849 2832 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.45 % Allowed : 15.71 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.22 (0.18), residues: 2140 helix: 1.26 (0.19), residues: 804 sheet: -0.20 (0.25), residues: 438 loop : -1.41 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 775 TYR 0.016 0.001 TYR C 561 PHE 0.016 0.001 PHE A 261 TRP 0.010 0.001 TRP C 819 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (18101) covalent geometry : angle 0.58306 / 0.30 (24664) hydrogen bonds : bond 0.03943 / 2.55 ( 759) hydrogen bonds : angle 4.63679 / 3.43 ( 2180) metal coordination : bond 0.00573 / 0.37 ( 12) metal coordination : angle 4.39723 / 2.41 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.7229 (mmm) cc_final: 0.6646 (mtp) REVERT: C 600 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7127 (tt) REVERT: D 73 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8000 (tptp) REVERT: A 447 MET cc_start: 0.0353 (ptt) cc_final: -0.0313 (ttp) REVERT: A 706 MET cc_start: 0.3282 (tpt) cc_final: 0.2753 (tpt) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 0.1185 time to fit residues: 34.7282 Evaluate side-chains 176 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 1081 PHE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 210 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 36 optimal weight: 0.0270 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 55 GLN D 78 GLN ** A 304 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.149579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116981 restraints weight = 33690.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117451 restraints weight = 27567.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118218 restraints weight = 21384.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118413 restraints weight = 16646.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118669 restraints weight = 15860.692| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18113 Z= 0.120 Angle : 0.574 9.726 24682 Z= 0.290 Chirality : 0.044 0.295 2825 Planarity : 0.004 0.041 3067 Dihedral : 12.685 178.968 2832 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 15.98 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.15 (0.19), residues: 2140 helix: 1.27 (0.19), residues: 811 sheet: -0.12 (0.25), residues: 433 loop : -1.37 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1053 TYR 0.013 0.001 TYR A 4 PHE 0.021 0.001 PHE A 261 TRP 0.010 0.001 TRP C1055 HIS 0.008 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (18101) covalent geometry : angle 0.56331 / 0.29 (24664) hydrogen bonds : bond 0.03686 / 2.38 ( 759) hydrogen bonds : angle 4.60707 / 3.41 ( 2180) metal coordination : bond 0.00484 / 0.32 ( 12) metal coordination : angle 4.10535 / 2.25 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.09 seconds wall clock time: 39 minutes 19.24 seconds (2359.24 seconds total)