Starting phenix.real_space_refine on Thu Feb 5 14:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1o_61977/02_2026/9k1o_61977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1o_61977/02_2026/9k1o_61977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k1o_61977/02_2026/9k1o_61977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1o_61977/02_2026/9k1o_61977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k1o_61977/02_2026/9k1o_61977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1o_61977/02_2026/9k1o_61977.map" } resolution = 3.3 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= 0.003 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 34 5.49 5 S 102 5.16 5 C 11175 2.51 5 N 3066 2.21 5 O 3383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17763 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: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 277 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 11} Chain: "H" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 15} 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 82.355 63.474 41.517 1.00 30.78 S ATOM 6671 SG CYS D 26 79.444 61.590 42.903 1.00 34.30 S ATOM 6918 SG CYS D 58 81.762 63.347 45.384 1.00 22.00 S ATOM 6939 SG CYS D 61 83.171 60.470 43.442 1.00 30.94 S ATOM 6560 SG CYS D 11 83.394 59.540 60.255 1.00 24.61 S ATOM 6823 SG CYS D 46 83.228 63.416 61.053 1.00 22.42 S ATOM 6846 SG CYS D 49 84.408 62.282 57.735 1.00 31.03 S ATOM 7117 SG CYS D 85 80.733 61.603 58.917 1.00 18.49 S ATOM 6698 SG CYS D 30 69.567 60.780 49.261 1.00 22.27 S ATOM 6719 SG CYS D 33 67.419 57.729 48.562 1.00 31.80 S ATOM 7014 SG CYS D 72 65.739 61.021 49.166 1.00 28.41 S ATOM 7038 SG CYS D 75 67.299 59.351 52.067 1.00 41.46 S Time building chain proxies: 4.66, per 1000 atoms: 0.26 Number of scatterers: 17763 At special positions: 0 Unit cell: (134.2, 146.3, 144.1, 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 34 15.00 O 3383 8.00 N 3066 7.00 C 11175 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: 1.78 Conformation dependent library (CDL) restraints added in 999.6 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 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 49 " 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: 78 helices and 27 sheets defined 41.2% alpha, 19.3% beta 9 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'C' and resid 508 through 522 Processing helix chain 'C' and resid 522 through 527 removed outlier: 3.509A 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 561 removed outlier: 3.978A pdb=" N TYR C 561 " --> pdb=" O ASP C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 579 removed outlier: 3.920A pdb=" N VAL C 577 " --> pdb=" O LYS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 583 removed outlier: 3.630A pdb=" N ILE C 583 " --> pdb=" O PRO C 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 580 through 583' Processing helix chain 'C' and resid 586 through 604 Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 621 through 638 Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.651A pdb=" N LYS C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 676 removed outlier: 4.383A pdb=" N ARG C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 676 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 680 removed outlier: 3.915A pdb=" N LEU C 680 " --> pdb=" O CYS C 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 677 through 680' Processing helix chain 'C' and resid 682 through 692 removed outlier: 3.722A pdb=" N LEU C 686 " --> pdb=" O HIS C 682 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 696 removed outlier: 3.895A pdb=" N ASP C 696 " --> pdb=" O GLY C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 693 through 696' Processing helix chain 'C' and resid 698 through 716 Processing helix chain 'C' and resid 720 through 725 removed outlier: 3.508A pdb=" N PHE C 724 " --> pdb=" O GLY C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 removed outlier: 3.578A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 736 " --> pdb=" O TRP C 732 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 737 " --> pdb=" O LYS C 733 " (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 777 removed outlier: 3.859A pdb=" N GLU C 768 " --> pdb=" O TYR C 764 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG C 775 " --> pdb=" O LEU C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 798 Processing helix chain 'C' and resid 802 through 810 removed outlier: 3.552A pdb=" N ILE C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 818 removed outlier: 3.786A pdb=" N LYS C 816 " --> pdb=" O PRO C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 removed outlier: 3.543A pdb=" N ALA C 824 " --> pdb=" O GLN C 820 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 845 Processing helix chain 'C' and resid 845 through 852 removed outlier: 3.545A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 859 removed outlier: 3.676A pdb=" N LYS C 858 " --> pdb=" O ASP C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 880 removed outlier: 3.501A pdb=" N ASN C 878 " --> pdb=" O LYS C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 902 removed outlier: 3.857A pdb=" N GLN C 891 " --> pdb=" O LYS C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 922 removed outlier: 4.236A pdb=" N LEU C 911 " --> pdb=" O ASP C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 927 removed outlier: 3.604A pdb=" N LYS C 926 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Proline residue: C 927 - end of helix No H-bonds generated for 'chain 'C' and resid 923 through 927' Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.815A pdb=" N ASN C 942 " --> pdb=" O TRP C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 965 removed outlier: 5.130A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 981 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.537A pdb=" N SER C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1015 Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1053 through 1066 removed outlier: 4.140A pdb=" N ARG C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1088 removed outlier: 3.534A pdb=" N ARG C1074 " --> pdb=" O LYS C1070 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C1082 " --> pdb=" O VAL C1078 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C1087 " --> pdb=" O TYR C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1100 removed outlier: 3.513A pdb=" N ALA C1095 " --> pdb=" O HIS C1091 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 3.619A pdb=" N ARG C1109 " --> pdb=" O GLU C1105 " (cutoff:3.500A) removed outlier: 3.518A 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 1135 removed outlier: 3.509A pdb=" N LEU C1132 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1138 No H-bonds generated for 'chain 'C' and resid 1136 through 1138' Processing helix chain 'C' and resid 1140 through 1159 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.997A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.745A pdb=" N VAL C1169 " --> pdb=" O TYR C1165 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.739A pdb=" N LEU C1208 " --> pdb=" O CYS C1204 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C1210 " --> pdb=" O ASP C1206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C1211 " --> pdb=" O SER C1207 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C1212 " --> pdb=" O LEU C1208 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN C1213 " --> pdb=" O ASN C1209 " (cutoff:3.500A) removed outlier: 4.130A 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 removed outlier: 3.962A pdb=" N VAL C1239 " --> pdb=" O GLU C1235 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C1240 " --> pdb=" O GLY C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 4.028A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1259 through 1275 removed outlier: 3.850A pdb=" N GLY C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1281 Processing helix chain 'C' and resid 1297 through 1302 removed outlier: 3.678A pdb=" N LEU C1300 " --> pdb=" O ARG C1297 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C1302 " --> pdb=" O GLU C1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 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 104 removed outlier: 3.743A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.618A pdb=" N ARG A 432 " --> pdb=" O ARG A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.768A pdb=" N CYS A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 removed outlier: 3.749A pdb=" N ALA A 827 " --> pdb=" O MET A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 removed outlier: 4.364A 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 1134 through 1152 removed outlier: 3.829A pdb=" N HIS A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1176 through 1180 Processing helix chain 'A' and resid 1181 through 1185 Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.806A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 removed outlier: 3.597A pdb=" N TYR B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 47 through 57 Processing helix chain 'B' and resid 60 through 72 Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.892A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 45 " --> pdb=" O ALA D 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.226A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 3.740A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A1120 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1117 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.533A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 54 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ARG A 42 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR A 52 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A 44 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 50 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.725A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 87 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A 104 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 89 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.824A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.967A pdb=" N LYS A 137 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 162 " --> pdb=" O LYS A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.078A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 232 through 238 removed outlier: 7.209A pdb=" N CYS A 251 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 235 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 249 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR A 237 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY A 247 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.436A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 287 through 293 removed outlier: 4.251A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 302 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 331 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 287 through 293 removed outlier: 4.251A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 302 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 336 through 342 removed outlier: 4.258A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 350 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU A 358 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.575A pdb=" N VAL A 777 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 445 through 451 removed outlier: 6.424A pdb=" N GLU A 446 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 766 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA A 448 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 764 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.069A pdb=" N ALA A 458 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 475 " --> pdb=" O TRP A 460 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 462 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 486 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 492 " --> pdb=" O SER A 486 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.738A pdb=" N GLN A 518 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 525 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.561A 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 549 removed outlier: 4.365A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 557 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 564 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 567 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 575 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 590 through 592 removed outlier: 3.715A 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 removed outlier: 6.798A pdb=" N GLY A 668 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 640 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASN A 666 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE A 642 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR A 664 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 669 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 702 through 706 removed outlier: 3.541A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 785 through 790 removed outlier: 6.661A pdb=" N THR A 802 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 787 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 886 through 894 removed outlier: 6.230A pdb=" N ALA A 888 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 910 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 890 " --> pdb=" O GLY A 908 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 905 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 923 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 943 " --> pdb=" O VAL A 925 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS A 941 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 953 through 955 removed outlier: 3.789A pdb=" N VAL A 959 " --> pdb=" O TYR A 970 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.557A 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: 3.878A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N GLN A1087 " --> pdb=" O ILE A1022 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A1024 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.907A pdb=" N CYS A1054 " --> pdb=" O GLY A1046 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5715 1.34 - 1.46: 3203 1.46 - 1.58: 9046 1.58 - 1.70: 66 1.70 - 1.82: 157 Bond restraints: 18187 Sorted by residual: bond pdb=" C GLU C 579 " pdb=" N PRO C 580 " ideal model delta sigma weight residual 1.337 1.368 -0.032 9.80e-03 1.04e+04 1.04e+01 bond pdb=" C3' G H 8 " pdb=" O3' G H 8 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.70e+00 bond pdb=" CG1 ILE C 872 " pdb=" CD1 ILE C 872 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.48e+00 bond pdb=" N LYS C 943 " pdb=" CA LYS C 943 " ideal model delta sigma weight residual 1.461 1.476 -0.015 1.49e-02 4.50e+03 1.03e+00 bond pdb=" N GLU C 980 " pdb=" CA GLU C 980 " ideal model delta sigma weight residual 1.458 1.471 -0.013 1.33e-02 5.65e+03 9.88e-01 ... (remaining 18182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 24490 1.96 - 3.92: 252 3.92 - 5.88: 48 5.88 - 7.84: 5 7.84 - 9.80: 4 Bond angle restraints: 24799 Sorted by residual: angle pdb=" C ASN C 942 " pdb=" N LYS C 943 " pdb=" CA LYS C 943 " ideal model delta sigma weight residual 122.40 130.29 -7.89 1.45e+00 4.76e-01 2.96e+01 angle pdb=" C GLY C 640 " pdb=" N ILE C 641 " pdb=" CA ILE C 641 " ideal model delta sigma weight residual 120.33 124.06 -3.73 8.00e-01 1.56e+00 2.17e+01 angle pdb=" C3' G H 8 " pdb=" O3' G H 8 " pdb=" P A H 9 " ideal model delta sigma weight residual 120.20 125.45 -5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N GLU C 980 " pdb=" CA GLU C 980 " pdb=" CB GLU C 980 " ideal model delta sigma weight residual 110.39 116.19 -5.80 1.66e+00 3.63e-01 1.22e+01 angle pdb=" CB MET C 498 " pdb=" CG MET C 498 " pdb=" SD MET C 498 " ideal model delta sigma weight residual 112.70 122.50 -9.80 3.00e+00 1.11e-01 1.07e+01 ... (remaining 24794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 10837 35.70 - 71.39: 174 71.39 - 107.09: 24 107.09 - 142.78: 1 142.78 - 178.48: 1 Dihedral angle restraints: 11037 sinusoidal: 4765 harmonic: 6272 Sorted by residual: dihedral pdb=" CA GLU C 809 " pdb=" C GLU C 809 " pdb=" N ILE C 810 " pdb=" CA ILE C 810 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+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 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C4' G H 8 " pdb=" C3' G H 8 " pdb=" O3' G H 8 " pdb=" P A H 9 " ideal model delta sinusoidal sigma weight residual 250.00 71.52 178.48 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 11034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2123 0.038 - 0.077: 461 0.077 - 0.115: 222 0.115 - 0.154: 28 0.154 - 0.192: 6 Chirality restraints: 2840 Sorted by residual: chirality pdb=" C3' G H 8 " pdb=" C4' G H 8 " pdb=" O3' G H 8 " pdb=" C2' G H 8 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.22e-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 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA GLU D 101 " pdb=" N GLU D 101 " pdb=" C GLU D 101 " pdb=" CB GLU D 101 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 2837 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 847 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 848 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 848 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 848 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1191 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C LYS A1191 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS A1191 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A1192 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 777 " -0.012 2.00e-02 2.50e+03 1.38e-02 3.32e+00 pdb=" CG PHE C 777 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 777 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 777 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 777 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 777 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 777 " -0.001 2.00e-02 2.50e+03 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2480 2.76 - 3.29: 16213 3.29 - 3.83: 27875 3.83 - 4.36: 31261 4.36 - 4.90: 55939 Nonbonded interactions: 133768 Sorted by model distance: nonbonded pdb=" OH TYR C 979 " pdb=" OD2 ASP C1015 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A 197 " pdb=" OE1 GLU A 199 " model vdw 2.251 3.040 nonbonded pdb=" O2' G H 14 " pdb=" OP1 C H 15 " model vdw 2.270 3.040 nonbonded pdb=" OD2 ASP C1278 " pdb=" OH TYR A1166 " model vdw 2.273 3.040 nonbonded pdb=" NH2 ARG C1106 " pdb=" OP2 U G 22 " model vdw 2.275 3.120 ... (remaining 133763 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 individual isotropic 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: 1.930 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.360 Find NCS groups from input model: 0.080 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 0.048 18199 Z= 0.104 Angle : 0.528 9.796 24817 Z= 0.278 Chirality : 0.041 0.192 2840 Planarity : 0.003 0.051 3070 Dihedral : 13.744 178.476 6997 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 0.06 (0.19), residues: 2140 helix: 1.59 (0.20), residues: 741 sheet: 0.20 (0.27), residues: 447 loop : -1.31 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1214 TYR 0.018 0.001 TYR C 830 PHE 0.032 0.001 PHE C 777 TRP 0.021 0.001 TRP C 658 HIS 0.002 0.000 HIS C 973 Details of bonding type rmsd covalent geometry : bond 0.00204 (18187) covalent geometry : angle 0.51609 (24799) hydrogen bonds : bond 0.19833 ( 764) hydrogen bonds : angle 7.08442 ( 2139) metal coordination : bond 0.00324 ( 12) metal coordination : angle 4.09141 ( 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 278 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.681 Fit side-chains REVERT: C 560 LEU cc_start: 0.8243 (tp) cc_final: 0.7987 (tp) REVERT: C 827 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.5919 (ttt90) REVERT: C 876 MET cc_start: 0.6904 (mmm) cc_final: 0.6657 (mtp) REVERT: A 217 LEU cc_start: 0.7133 (mm) cc_final: 0.6678 (mt) REVERT: A 233 ASN cc_start: 0.6944 (p0) cc_final: 0.6707 (p0) REVERT: A 645 MET cc_start: 0.0402 (mmp) cc_final: -0.0230 (ppp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1389 time to fit residues: 59.2296 Evaluate side-chains 210 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 HIS A 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.191913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145844 restraints weight = 23270.848| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.49 r_work: 0.3400 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18199 Z= 0.145 Angle : 0.583 9.300 24817 Z= 0.296 Chirality : 0.044 0.214 2840 Planarity : 0.004 0.052 3070 Dihedral : 11.092 173.684 2846 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.02 % Allowed : 6.70 % Favored : 92.28 % 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: -0.04 (0.18), residues: 2140 helix: 1.58 (0.20), residues: 757 sheet: -0.06 (0.26), residues: 450 loop : -1.38 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 948 TYR 0.018 0.001 TYR C 830 PHE 0.014 0.001 PHE A 234 TRP 0.026 0.002 TRP A 720 HIS 0.006 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00336 (18187) covalent geometry : angle 0.56304 (24799) hydrogen bonds : bond 0.04347 ( 764) hydrogen bonds : angle 5.15541 ( 2139) metal coordination : bond 0.00662 ( 12) metal coordination : angle 5.66356 ( 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 239 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.650 Fit side-chains REVERT: C 499 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7737 (ptmm) REVERT: C 540 MET cc_start: 0.6305 (ptt) cc_final: 0.5128 (mmm) REVERT: C 609 MET cc_start: 0.8620 (ptt) cc_final: 0.8376 (ptt) REVERT: C 827 ARG cc_start: 0.7337 (ttp-170) cc_final: 0.5862 (ttt90) REVERT: C 867 MET cc_start: 0.7934 (ttp) cc_final: 0.7547 (ttp) REVERT: C 1002 ASN cc_start: 0.7370 (m110) cc_final: 0.6886 (m110) REVERT: C 1133 MET cc_start: 0.8201 (mmm) cc_final: 0.7922 (mmm) REVERT: C 1135 GLU cc_start: 0.8209 (tp30) cc_final: 0.7960 (tp30) REVERT: D 101 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 233 ASN cc_start: 0.7522 (p0) cc_final: 0.7312 (p0) REVERT: A 359 TYR cc_start: 0.8831 (m-80) cc_final: 0.8546 (m-80) REVERT: A 583 MET cc_start: 0.2602 (mpp) cc_final: 0.1326 (mmm) REVERT: A 645 MET cc_start: 0.0488 (mmp) cc_final: -0.0298 (ppp) REVERT: A 1135 HIS cc_start: 0.5301 (m90) cc_final: 0.5034 (t70) outliers start: 19 outliers final: 12 residues processed: 230 average time/residue: 0.1453 time to fit residues: 50.5153 Evaluate side-chains 212 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain B residue 19 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 HIS C1107 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.187268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141330 restraints weight = 23491.912| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.56 r_work: 0.3320 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18199 Z= 0.172 Angle : 0.604 12.163 24817 Z= 0.305 Chirality : 0.044 0.214 2840 Planarity : 0.004 0.048 3070 Dihedral : 11.220 173.967 2846 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.13 % Allowed : 9.49 % Favored : 89.38 % 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: -0.19 (0.18), residues: 2140 helix: 1.47 (0.20), residues: 755 sheet: -0.17 (0.25), residues: 448 loop : -1.46 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 495 TYR 0.015 0.001 TYR C 764 PHE 0.019 0.002 PHE A 955 TRP 0.018 0.002 TRP A 720 HIS 0.007 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00414 (18187) covalent geometry : angle 0.57933 (24799) hydrogen bonds : bond 0.04723 ( 764) hydrogen bonds : angle 4.85699 ( 2139) metal coordination : bond 0.00791 ( 12) metal coordination : angle 6.35973 ( 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 236 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.592 Fit side-chains REVERT: C 495 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8582 (mmm160) REVERT: C 540 MET cc_start: 0.6229 (ptt) cc_final: 0.5044 (mmm) REVERT: C 579 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6129 (pm20) REVERT: C 1135 GLU cc_start: 0.8252 (tp30) cc_final: 0.7983 (tp30) REVERT: A 359 TYR cc_start: 0.8830 (m-80) cc_final: 0.8602 (m-80) REVERT: A 645 MET cc_start: 0.0514 (mmp) cc_final: -0.0248 (ppp) REVERT: A 720 TRP cc_start: 0.6446 (m100) cc_final: 0.5725 (m100) outliers start: 21 outliers final: 14 residues processed: 227 average time/residue: 0.1424 time to fit residues: 49.3596 Evaluate side-chains 211 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1127 THR Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 30.0000 chunk 188 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN C 662 HIS C 778 GLN A 264 GLN ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.186335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140371 restraints weight = 23241.117| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.57 r_work: 0.3305 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18199 Z= 0.170 Angle : 0.589 11.750 24817 Z= 0.299 Chirality : 0.044 0.217 2840 Planarity : 0.004 0.047 3070 Dihedral : 11.267 173.287 2846 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.66 % Allowed : 11.42 % Favored : 86.92 % 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: -0.30 (0.18), residues: 2140 helix: 1.44 (0.19), residues: 748 sheet: -0.19 (0.25), residues: 459 loop : -1.61 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 948 TYR 0.019 0.001 TYR C 830 PHE 0.016 0.002 PHE A 955 TRP 0.011 0.002 TRP B 29 HIS 0.006 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00410 (18187) covalent geometry : angle 0.56781 (24799) hydrogen bonds : bond 0.04517 ( 764) hydrogen bonds : angle 4.70058 ( 2139) metal coordination : bond 0.00772 ( 12) metal coordination : angle 5.89253 ( 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 244 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.670 Fit side-chains REVERT: C 540 MET cc_start: 0.6244 (ptt) cc_final: 0.5062 (mmm) REVERT: C 579 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6001 (pm20) REVERT: C 827 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7197 (tmm-80) REVERT: C 947 VAL cc_start: 0.8539 (m) cc_final: 0.8321 (p) REVERT: C 1045 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8177 (mmm160) REVERT: D 101 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: A 331 ASP cc_start: 0.7356 (m-30) cc_final: 0.6964 (m-30) REVERT: A 359 TYR cc_start: 0.8802 (m-80) cc_final: 0.8574 (m-80) REVERT: A 583 MET cc_start: 0.2810 (mpp) cc_final: 0.1532 (mmm) REVERT: A 645 MET cc_start: 0.0395 (mmp) cc_final: -0.0368 (ppp) REVERT: A 720 TRP cc_start: 0.6454 (m100) cc_final: 0.5883 (m100) REVERT: A 1128 ILE cc_start: 0.8637 (pt) cc_final: 0.8264 (mt) REVERT: A 1195 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8284 (mp0) outliers start: 31 outliers final: 21 residues processed: 228 average time/residue: 0.1439 time to fit residues: 50.2585 Evaluate side-chains 222 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1127 THR Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 19 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.189108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143177 restraints weight = 23265.613| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.54 r_work: 0.3346 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18199 Z= 0.107 Angle : 0.536 8.371 24817 Z= 0.273 Chirality : 0.042 0.213 2840 Planarity : 0.004 0.045 3070 Dihedral : 11.168 173.263 2846 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.77 % Allowed : 12.65 % Favored : 85.58 % 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: -0.12 (0.18), residues: 2140 helix: 1.64 (0.20), residues: 748 sheet: -0.12 (0.24), residues: 467 loop : -1.54 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 495 TYR 0.018 0.001 TYR C 764 PHE 0.011 0.001 PHE A1024 TRP 0.009 0.001 TRP C 658 HIS 0.003 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00242 (18187) covalent geometry : angle 0.52174 (24799) hydrogen bonds : bond 0.03528 ( 764) hydrogen bonds : angle 4.45917 ( 2139) metal coordination : bond 0.00441 ( 12) metal coordination : angle 4.55795 ( 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 254 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: C 495 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8486 (mmm160) REVERT: C 540 MET cc_start: 0.6151 (ptt) cc_final: 0.4950 (mmm) REVERT: C 579 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: C 827 ARG cc_start: 0.7633 (ttp-170) cc_final: 0.6081 (tpt-90) REVERT: C 864 TYR cc_start: 0.8148 (t80) cc_final: 0.7825 (t80) REVERT: C 1045 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8140 (mmm160) REVERT: C 1135 GLU cc_start: 0.8246 (tp30) cc_final: 0.7920 (tp30) REVERT: D 101 GLU cc_start: 0.7438 (mp0) cc_final: 0.6819 (mp0) REVERT: A 331 ASP cc_start: 0.7190 (m-30) cc_final: 0.6983 (m-30) REVERT: A 359 TYR cc_start: 0.8728 (m-80) cc_final: 0.8504 (m-80) REVERT: A 583 MET cc_start: 0.2382 (mpp) cc_final: 0.1174 (mmm) REVERT: A 645 MET cc_start: 0.0284 (mmp) cc_final: -0.0301 (ppp) REVERT: A 720 TRP cc_start: 0.6363 (m100) cc_final: 0.5843 (m100) REVERT: A 1128 ILE cc_start: 0.8581 (pt) cc_final: 0.8220 (mt) REVERT: A 1185 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7435 (ttm) outliers start: 33 outliers final: 19 residues processed: 238 average time/residue: 0.1285 time to fit residues: 47.2774 Evaluate side-chains 227 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 954 LEU Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 1 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 20 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 GLN C 698 GLN C 778 GLN C 842 ASN A 518 GLN A 804 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.185877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140464 restraints weight = 23273.973| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.47 r_work: 0.3289 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18199 Z= 0.174 Angle : 0.595 10.794 24817 Z= 0.301 Chirality : 0.044 0.218 2840 Planarity : 0.004 0.045 3070 Dihedral : 11.267 172.983 2846 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.09 % Allowed : 13.35 % Favored : 84.56 % 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: -0.30 (0.18), residues: 2140 helix: 1.47 (0.20), residues: 748 sheet: -0.20 (0.25), residues: 462 loop : -1.62 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 429 TYR 0.016 0.001 TYR C 764 PHE 0.016 0.002 PHE A 955 TRP 0.011 0.002 TRP B 29 HIS 0.006 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00421 (18187) covalent geometry : angle 0.57557 (24799) hydrogen bonds : bond 0.04464 ( 764) hydrogen bonds : angle 4.56058 ( 2139) metal coordination : bond 0.00694 ( 12) metal coordination : angle 5.60934 ( 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 249 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: C 495 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8454 (mmm160) REVERT: C 540 MET cc_start: 0.6132 (ptt) cc_final: 0.4942 (mmm) REVERT: C 579 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: C 775 ARG cc_start: 0.7406 (ptt90) cc_final: 0.7084 (ptt90) REVERT: C 827 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.6104 (tpt-90) REVERT: C 864 TYR cc_start: 0.8182 (t80) cc_final: 0.7838 (t80) REVERT: C 1045 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8198 (mmm160) REVERT: C 1054 GLU cc_start: 0.8118 (pm20) cc_final: 0.7852 (pm20) REVERT: C 1175 ASP cc_start: 0.8563 (t0) cc_final: 0.8270 (t70) REVERT: D 101 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 331 ASP cc_start: 0.7318 (m-30) cc_final: 0.7084 (m-30) REVERT: A 359 TYR cc_start: 0.8798 (m-80) cc_final: 0.8586 (m-80) REVERT: A 583 MET cc_start: 0.2150 (mpp) cc_final: 0.1088 (mmm) REVERT: A 645 MET cc_start: 0.0489 (mmp) cc_final: -0.0135 (ppp) REVERT: A 720 TRP cc_start: 0.6429 (m100) cc_final: 0.5895 (m100) REVERT: A 1128 ILE cc_start: 0.8606 (pt) cc_final: 0.8253 (mt) outliers start: 39 outliers final: 29 residues processed: 234 average time/residue: 0.1294 time to fit residues: 46.7460 Evaluate side-chains 232 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1127 THR Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 179 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.187729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141992 restraints weight = 23376.075| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.54 r_work: 0.3320 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18199 Z= 0.121 Angle : 0.555 10.120 24817 Z= 0.281 Chirality : 0.042 0.213 2840 Planarity : 0.004 0.044 3070 Dihedral : 11.209 173.014 2846 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 13.89 % Favored : 84.29 % 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: -0.24 (0.18), residues: 2140 helix: 1.55 (0.20), residues: 747 sheet: -0.09 (0.25), residues: 440 loop : -1.64 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 924 TYR 0.017 0.001 TYR C 764 PHE 0.013 0.001 PHE A1024 TRP 0.008 0.001 TRP A1011 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00284 (18187) covalent geometry : angle 0.54008 (24799) hydrogen bonds : bond 0.03721 ( 764) hydrogen bonds : angle 4.41411 ( 2139) metal coordination : bond 0.00508 ( 12) metal coordination : angle 4.70696 ( 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 244 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 495 ARG cc_start: 0.8740 (mmm160) cc_final: 0.8483 (mmm160) REVERT: C 579 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: C 675 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7174 (mmm) REVERT: C 775 ARG cc_start: 0.7355 (ptt90) cc_final: 0.7029 (ptt90) REVERT: C 864 TYR cc_start: 0.8058 (t80) cc_final: 0.7755 (t80) REVERT: C 1045 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8196 (mmm160) REVERT: C 1175 ASP cc_start: 0.8593 (t0) cc_final: 0.8275 (t70) REVERT: D 101 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 53 LEU cc_start: 0.8402 (mt) cc_final: 0.7631 (pp) REVERT: A 181 MET cc_start: 0.8395 (mmm) cc_final: 0.7938 (mmm) REVERT: A 331 ASP cc_start: 0.7268 (m-30) cc_final: 0.7053 (m-30) REVERT: A 359 TYR cc_start: 0.8758 (m-80) cc_final: 0.8527 (m-80) REVERT: A 583 MET cc_start: 0.2455 (mpp) cc_final: 0.1182 (mmm) REVERT: A 645 MET cc_start: 0.0496 (mmp) cc_final: -0.0117 (ppp) REVERT: A 720 TRP cc_start: 0.6428 (m100) cc_final: 0.5891 (m100) REVERT: A 1128 ILE cc_start: 0.8591 (pt) cc_final: 0.8282 (mt) outliers start: 34 outliers final: 25 residues processed: 227 average time/residue: 0.1395 time to fit residues: 48.7771 Evaluate side-chains 231 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 143 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.187519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142144 restraints weight = 23348.396| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.41 r_work: 0.3312 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18199 Z= 0.125 Angle : 0.557 10.700 24817 Z= 0.283 Chirality : 0.042 0.213 2840 Planarity : 0.004 0.045 3070 Dihedral : 11.194 172.920 2846 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.55 % Allowed : 14.37 % Favored : 84.08 % 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: -0.21 (0.18), residues: 2140 helix: 1.58 (0.20), residues: 747 sheet: -0.07 (0.25), residues: 445 loop : -1.63 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 924 TYR 0.017 0.001 TYR C 764 PHE 0.012 0.001 PHE A1024 TRP 0.008 0.001 TRP A1011 HIS 0.004 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00294 (18187) covalent geometry : angle 0.54234 (24799) hydrogen bonds : bond 0.03763 ( 764) hydrogen bonds : angle 4.38078 ( 2139) metal coordination : bond 0.00504 ( 12) metal coordination : angle 4.69140 ( 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 244 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 579 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.6028 (pm20) REVERT: C 675 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7267 (mmm) REVERT: C 775 ARG cc_start: 0.7262 (ptt90) cc_final: 0.6944 (ptt90) REVERT: C 827 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.6296 (tpt-90) REVERT: C 864 TYR cc_start: 0.8030 (t80) cc_final: 0.7738 (t80) REVERT: C 1054 GLU cc_start: 0.8034 (pm20) cc_final: 0.7780 (pm20) REVERT: C 1175 ASP cc_start: 0.8566 (t0) cc_final: 0.8259 (t70) REVERT: D 101 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 53 LEU cc_start: 0.8413 (mt) cc_final: 0.7644 (pp) REVERT: A 181 MET cc_start: 0.8408 (mmm) cc_final: 0.7935 (mmm) REVERT: A 331 ASP cc_start: 0.7280 (m-30) cc_final: 0.7032 (m-30) REVERT: A 359 TYR cc_start: 0.8764 (m-80) cc_final: 0.8535 (m-80) REVERT: A 583 MET cc_start: 0.2424 (mpp) cc_final: 0.1123 (mmm) REVERT: A 645 MET cc_start: 0.0475 (mmp) cc_final: -0.0130 (ppp) REVERT: A 720 TRP cc_start: 0.6482 (m100) cc_final: 0.5914 (m100) REVERT: A 1018 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6936 (tm-30) REVERT: A 1128 ILE cc_start: 0.8592 (pt) cc_final: 0.8295 (mt) outliers start: 29 outliers final: 23 residues processed: 231 average time/residue: 0.1393 time to fit residues: 49.6154 Evaluate side-chains 231 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 44 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 172 optimal weight: 0.0000 chunk 203 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.0040 chunk 134 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 23 optimal weight: 0.0270 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 518 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 = 0.4273 r_free = 0.4273 target = 0.188281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143231 restraints weight = 23274.713| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.39 r_work: 0.3326 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18199 Z= 0.117 Angle : 0.562 11.645 24817 Z= 0.284 Chirality : 0.042 0.212 2840 Planarity : 0.004 0.052 3070 Dihedral : 11.171 172.772 2846 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.72 % Allowed : 14.53 % 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: -0.17 (0.18), residues: 2140 helix: 1.61 (0.20), residues: 747 sheet: -0.07 (0.25), residues: 447 loop : -1.60 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 495 TYR 0.023 0.001 TYR C 830 PHE 0.011 0.001 PHE A1024 TRP 0.008 0.001 TRP A1011 HIS 0.004 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00273 (18187) covalent geometry : angle 0.54947 (24799) hydrogen bonds : bond 0.03585 ( 764) hydrogen bonds : angle 4.34077 ( 2139) metal coordination : bond 0.00457 ( 12) metal coordination : angle 4.43898 ( 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 243 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: C 540 MET cc_start: 0.6182 (ptt) cc_final: 0.5167 (tpt) REVERT: C 579 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6144 (pm20) REVERT: C 675 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7305 (mmt) REVERT: C 827 ARG cc_start: 0.7610 (ttt-90) cc_final: 0.6253 (tpt-90) REVERT: C 864 TYR cc_start: 0.8063 (t80) cc_final: 0.7834 (t80) REVERT: C 1175 ASP cc_start: 0.8580 (t0) cc_final: 0.8295 (t70) REVERT: A 53 LEU cc_start: 0.8407 (mt) cc_final: 0.7681 (pp) REVERT: A 331 ASP cc_start: 0.7233 (m-30) cc_final: 0.6992 (m-30) REVERT: A 359 TYR cc_start: 0.8753 (m-80) cc_final: 0.8535 (m-80) REVERT: A 583 MET cc_start: 0.2440 (mpp) cc_final: 0.1119 (mmm) REVERT: A 645 MET cc_start: 0.0480 (mmp) cc_final: -0.0124 (ppp) REVERT: A 720 TRP cc_start: 0.6611 (m100) cc_final: 0.6052 (m100) REVERT: A 1128 ILE cc_start: 0.8602 (pt) cc_final: 0.8334 (mt) outliers start: 32 outliers final: 26 residues processed: 230 average time/residue: 0.1330 time to fit residues: 47.4946 Evaluate side-chains 236 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 44 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN A 775 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.187501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141736 restraints weight = 23227.623| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.48 r_work: 0.3320 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18199 Z= 0.130 Angle : 0.581 12.129 24817 Z= 0.295 Chirality : 0.043 0.214 2840 Planarity : 0.004 0.044 3070 Dihedral : 11.185 172.682 2846 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.55 % Allowed : 14.80 % Favored : 83.65 % 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: 1.52 (0.20), residues: 753 sheet: -0.09 (0.25), residues: 447 loop : -1.59 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 495 TYR 0.018 0.001 TYR C 764 PHE 0.012 0.001 PHE A 234 TRP 0.008 0.001 TRP A1011 HIS 0.005 0.001 HIS A 941 Details of bonding type rmsd covalent geometry : bond 0.00308 (18187) covalent geometry : angle 0.56747 (24799) hydrogen bonds : bond 0.03778 ( 764) hydrogen bonds : angle 4.37458 ( 2139) metal coordination : bond 0.00508 ( 12) metal coordination : angle 4.66183 ( 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 238 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: C 495 ARG cc_start: 0.8774 (mmm160) cc_final: 0.8405 (mmm160) REVERT: C 540 MET cc_start: 0.6137 (ptt) cc_final: 0.5099 (tpt) REVERT: C 579 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: C 675 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7337 (mmt) REVERT: C 775 ARG cc_start: 0.7324 (ptt90) cc_final: 0.6998 (ptt90) REVERT: C 827 ARG cc_start: 0.7644 (ttt-90) cc_final: 0.6228 (tpt-90) REVERT: C 864 TYR cc_start: 0.8029 (t80) cc_final: 0.7777 (t80) REVERT: C 867 MET cc_start: 0.7927 (ttp) cc_final: 0.7420 (ttp) REVERT: C 1175 ASP cc_start: 0.8554 (t0) cc_final: 0.8260 (t70) REVERT: A 53 LEU cc_start: 0.8403 (mt) cc_final: 0.7650 (pp) REVERT: A 331 ASP cc_start: 0.7291 (m-30) cc_final: 0.7007 (m-30) REVERT: A 359 TYR cc_start: 0.8753 (m-80) cc_final: 0.8525 (m-80) REVERT: A 583 MET cc_start: 0.2499 (mpp) cc_final: 0.1181 (mmm) REVERT: A 645 MET cc_start: 0.0497 (mmp) cc_final: -0.0124 (ppp) REVERT: A 720 TRP cc_start: 0.6454 (m100) cc_final: 0.5864 (m100) REVERT: A 1128 ILE cc_start: 0.8586 (pt) cc_final: 0.8298 (mt) outliers start: 29 outliers final: 25 residues processed: 227 average time/residue: 0.1348 time to fit residues: 47.2566 Evaluate side-chains 231 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain C residue 1256 HIS Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 44 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 137 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 122 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 204 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 518 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 = 0.4287 r_free = 0.4287 target = 0.189650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143481 restraints weight = 23460.178| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.27 r_work: 0.3367 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18199 Z= 0.104 Angle : 0.558 12.629 24817 Z= 0.282 Chirality : 0.042 0.211 2840 Planarity : 0.004 0.046 3070 Dihedral : 11.118 172.624 2846 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 14.75 % Favored : 83.54 % 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: -0.11 (0.18), residues: 2140 helix: 1.62 (0.20), residues: 750 sheet: 0.02 (0.25), residues: 447 loop : -1.56 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 495 TYR 0.019 0.001 TYR C 830 PHE 0.010 0.001 PHE A1024 TRP 0.009 0.001 TRP C1055 HIS 0.003 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00234 (18187) covalent geometry : angle 0.54764 (24799) hydrogen bonds : bond 0.03228 ( 764) hydrogen bonds : angle 4.26994 ( 2139) metal coordination : bond 0.00370 ( 12) metal coordination : angle 3.96590 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4481.58 seconds wall clock time: 77 minutes 33.95 seconds (4653.95 seconds total)