Starting phenix.real_space_refine on Thu Sep 18 13:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5zya_6915/09_2025/5zya_6915.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zya_6915/09_2025/5zya_6915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5zya_6915/09_2025/5zya_6915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zya_6915/09_2025/5zya_6915.map" model { file = "/net/cci-nas-00/data/ceres_data/5zya_6915/09_2025/5zya_6915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zya_6915/09_2025/5zya_6915.cif" } resolution = 3.95 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 ------------------------------------------------------------------------------- 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= 0.007 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 K 1 8.98 5 Zn 3 6.06 5 S 102 5.16 5 C 10800 2.51 5 N 2895 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16957 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "C" Number of atoms: 6438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6438 Classifications: {'peptide': 809} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 774} Chain breaks: 1 Chain: "D" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 645 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "A" Number of atoms: 9280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9280 Classifications: {'peptide': 1183} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1122} Chain breaks: 5 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'9B0': 1} Classifications: {'undetermined': 1} 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7105 SG CYS D 23 30.112 90.456 66.528 1.00 68.38 S ATOM 7376 SG CYS D 58 33.151 91.184 64.701 1.00 63.42 S ATOM 7397 SG CYS D 61 29.986 92.741 63.750 1.00 65.46 S ATOM 7018 SG CYS D 11 43.982 98.304 55.595 1.00 71.87 S ATOM 7281 SG CYS D 46 46.263 97.192 59.934 1.00 62.04 S ATOM 7575 SG CYS D 85 45.777 95.371 56.868 1.00 67.32 S ATOM 7156 SG CYS D 30 38.525 81.746 57.804 1.00 52.14 S ATOM 7177 SG CYS D 33 37.070 80.142 54.160 1.00 47.74 S ATOM 7472 SG CYS D 72 39.458 78.230 56.015 1.00 44.18 S ATOM 7496 SG CYS D 75 40.699 80.609 53.666 1.00 43.95 S Time building chain proxies: 4.08, per 1000 atoms: 0.24 Number of scatterers: 16957 At special positions: 0 Unit cell: (132.2, 145.42, 125.59, 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 K 1 19.00 S 102 16.00 O 3156 8.00 N 2895 7.00 C 10800 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: 1.63 Conformation dependent library (CDL) restraints added in 755.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " Number of angles added : 6 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4012 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 30 sheets defined 36.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'C' and resid 491 through 497 Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 508 through 522 Processing helix chain 'C' and resid 522 through 527 Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.889A pdb=" N PHE C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 560 removed outlier: 3.516A pdb=" N LYS C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 578 Processing helix chain 'C' and resid 586 through 604 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 621 through 640 Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.741A pdb=" N LYS C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 676 Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 698 through 717 removed outlier: 4.306A pdb=" N ALA C 715 " --> pdb=" O ALA C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 removed outlier: 3.896A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG C 736 " --> pdb=" O TRP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 removed outlier: 3.767A pdb=" N ALA C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 776 removed outlier: 4.192A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 796 Processing helix chain 'C' and resid 802 through 810 Processing helix chain 'C' and resid 810 through 818 removed outlier: 3.572A pdb=" N PHE C 814 " --> pdb=" O ILE C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 845 removed outlier: 4.139A pdb=" N LYS C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 852 through 853 No H-bonds generated for 'chain 'C' and resid 852 through 853' Processing helix chain 'C' and resid 854 through 858 removed outlier: 3.658A pdb=" N LYS C 858 " --> pdb=" O ASP C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 888 through 902 removed outlier: 4.148A pdb=" N GLU C 902 " --> pdb=" O TYR C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 922 Processing helix chain 'C' and resid 923 through 925 No H-bonds generated for 'chain 'C' and resid 923 through 925' Processing helix chain 'C' and resid 928 through 941 removed outlier: 3.594A pdb=" N ILE C 932 " --> pdb=" O TYR C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 957 removed outlier: 3.826A pdb=" N GLN C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.619A pdb=" N MET C 962 " --> pdb=" O THR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 981 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.923A pdb=" N SER C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 removed outlier: 3.957A pdb=" N LYS C1025 " --> pdb=" O PRO C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1051 through 1064 removed outlier: 4.369A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1068 removed outlier: 3.793A pdb=" N ALA C1068 " --> pdb=" O LEU C1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1065 through 1068' Processing helix chain 'C' and resid 1070 through 1088 Processing helix chain 'C' and resid 1109 through 1123 Processing helix chain 'C' and resid 1127 through 1137 Processing helix chain 'C' and resid 1143 through 1159 Processing helix chain 'C' and resid 1160 through 1163 removed outlier: 3.734A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1163' Processing helix chain 'C' and resid 1168 through 1178 removed outlier: 3.678A pdb=" N LEU C1172 " --> pdb=" O ALA C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1199 Processing helix chain 'C' and resid 1205 through 1216 removed outlier: 3.866A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1219 No H-bonds generated for 'chain 'C' and resid 1217 through 1219' Processing helix chain 'C' and resid 1223 through 1242 Processing helix chain 'C' and resid 1242 through 1249 removed outlier: 3.861A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1275 removed outlier: 3.646A pdb=" N VAL C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1281 removed outlier: 3.900A pdb=" N ILE C1281 " --> pdb=" O ASP C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1301 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.636A pdb=" N ASP A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 194' Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 808 through 825 Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 1134 through 1152 removed outlier: 4.528A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1165 Processing helix chain 'A' and resid 1186 through 1195 Processing helix chain 'A' and resid 1200 through 1215 removed outlier: 3.860A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 9 through 10 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.821A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.743A pdb=" N CYS D 40 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.206A pdb=" N LEU A 3 " --> pdb=" O ILE A1174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 6 through 9 removed outlier: 6.743A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A1120 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.791A pdb=" N GLU A 39 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 54 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.225A pdb=" N SER A 64 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 66 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 78 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 87 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.947A pdb=" N MET A 98 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.691A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 165 through 167 removed outlier: 3.648A pdb=" N THR A 207 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 232 through 237 removed outlier: 4.895A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 251 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 236 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 249 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 248 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.387A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 293 through 294 removed outlier: 3.594A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.744A pdb=" N ILE A 310 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.981A pdb=" N ARG A 326 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 336 through 342 removed outlier: 4.074A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 350 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 358 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 407 through 413 removed outlier: 3.538A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 427 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 444 through 449 removed outlier: 6.320A pdb=" N ILE A 764 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 473 through 477 Processing sheet with id=AC3, first strand: chain 'A' and resid 507 through 510 removed outlier: 3.672A pdb=" N SER A 507 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 518 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 525 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 546 through 549 removed outlier: 3.730A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 554 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 564 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 587 through 589 removed outlier: 4.387A pdb=" N LEU A 609 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 629 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 640 through 643 removed outlier: 4.155A pdb=" N CYS A 641 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 666 " --> pdb=" O CYS A 641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 664 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 667 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.673A pdb=" N PHE A 702 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 722 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 785 through 790 removed outlier: 6.738A pdb=" N THR A 802 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 787 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 803 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N SER A 864 " --> pdb=" O GLN A 881 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN A 881 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 866 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU A 879 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 868 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 886 through 891 removed outlier: 3.519A pdb=" N ALA A 887 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 953 through 955 Processing sheet with id=AD2, first strand: chain 'A' and resid 990 through 995 removed outlier: 3.803A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A1020 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1037 through 1038 removed outlier: 3.787A pdb=" N ALA A1045 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4284 1.33 - 1.45: 3717 1.45 - 1.58: 9125 1.58 - 1.70: 6 1.70 - 1.83: 158 Bond restraints: 17290 Sorted by residual: bond pdb=" C17 9B0 C1401 " pdb=" C18 9B0 C1401 " ideal model delta sigma weight residual 1.337 1.516 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C6 9B0 C1401 " pdb=" C8 9B0 C1401 " ideal model delta sigma weight residual 1.542 1.720 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C14 9B0 C1401 " pdb=" C16 9B0 C1401 " ideal model delta sigma weight residual 1.344 1.518 -0.174 2.00e-02 2.50e+03 7.57e+01 bond pdb=" C11 9B0 C1401 " pdb=" C13 9B0 C1401 " ideal model delta sigma weight residual 1.540 1.693 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C34 9B0 C1401 " pdb=" C40 9B0 C1401 " ideal model delta sigma weight residual 1.542 1.654 -0.112 2.00e-02 2.50e+03 3.11e+01 ... (remaining 17285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.54: 23288 5.54 - 11.08: 124 11.08 - 16.62: 10 16.62 - 22.15: 3 22.15 - 27.69: 4 Bond angle restraints: 23429 Sorted by residual: angle pdb=" C35 9B0 C1401 " pdb=" C34 9B0 C1401 " pdb=" N2 9B0 C1401 " ideal model delta sigma weight residual 110.42 138.11 -27.69 3.00e+00 1.11e-01 8.52e+01 angle pdb=" C36 9B0 C1401 " pdb=" C37 9B0 C1401 " pdb=" C38 9B0 C1401 " ideal model delta sigma weight residual 115.94 143.34 -27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C37 9B0 C1401 " pdb=" C38 9B0 C1401 " pdb=" C39 9B0 C1401 " ideal model delta sigma weight residual 113.37 87.02 26.35 3.00e+00 1.11e-01 7.71e+01 angle pdb=" C34 9B0 C1401 " pdb=" C40 9B0 C1401 " pdb=" C39 9B0 C1401 " ideal model delta sigma weight residual 116.42 141.00 -24.58 3.00e+00 1.11e-01 6.71e+01 angle pdb=" N GLY C 740 " pdb=" CA GLY C 740 " pdb=" C GLY C 740 " ideal model delta sigma weight residual 110.29 119.21 -8.92 1.28e+00 6.10e-01 4.85e+01 ... (remaining 23424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 10252 24.14 - 48.29: 263 48.29 - 72.43: 15 72.43 - 96.57: 6 96.57 - 120.72: 6 Dihedral angle restraints: 10542 sinusoidal: 4315 harmonic: 6227 Sorted by residual: dihedral pdb=" CA GLN B 74 " pdb=" C GLN B 74 " pdb=" N PRO B 75 " pdb=" CA PRO B 75 " ideal model delta harmonic sigma weight residual -180.00 -143.25 -36.75 0 5.00e+00 4.00e-02 5.40e+01 dihedral pdb=" CA TYR C 719 " pdb=" C TYR C 719 " pdb=" N GLY C 720 " pdb=" CA GLY C 720 " ideal model delta harmonic sigma weight residual -180.00 -145.04 -34.96 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA ILE C 754 " pdb=" C ILE C 754 " pdb=" N PRO C 755 " pdb=" CA PRO C 755 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 10539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2503 0.123 - 0.246: 147 0.246 - 0.369: 8 0.369 - 0.492: 2 0.492 - 0.615: 2 Chirality restraints: 2662 Sorted by residual: chirality pdb=" C8 9B0 C1401 " pdb=" C6 9B0 C1401 " pdb=" C9 9B0 C1401 " pdb=" O5 9B0 C1401 " both_signs ideal model delta sigma weight residual False 2.50 1.88 0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" C13 9B0 C1401 " pdb=" C11 9B0 C1401 " pdb=" C14 9B0 C1401 " pdb=" O1 9B0 C1401 " both_signs ideal model delta sigma weight residual False -2.57 -3.08 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" C3 9B0 C1401 " pdb=" C2 9B0 C1401 " pdb=" C4 9B0 C1401 " pdb=" O3 9B0 C1401 " both_signs ideal model delta sigma weight residual False -2.37 -2.76 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 2659 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 9B0 C1401 " -0.130 2.00e-02 2.50e+03 7.49e-02 5.61e+01 pdb=" C2 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" O1 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" O2 9B0 C1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 9B0 C1401 " 0.012 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C14 9B0 C1401 " -0.065 2.00e-02 2.50e+03 pdb=" C15 9B0 C1401 " 0.027 2.00e-02 2.50e+03 pdb=" C16 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" C17 9B0 C1401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 754 " -0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO C 755 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 755 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 755 " -0.049 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.37: 31 2.37 - 3.06: 10214 3.06 - 3.75: 29015 3.75 - 4.45: 43512 4.45 - 5.14: 71152 Nonbonded interactions: 153924 Sorted by model distance: nonbonded pdb=" O LEU C1251 " pdb=" CD1 LEU C1254 " model vdw 1.673 3.460 nonbonded pdb=" O ALA C 762 " pdb=" OG1 THR C 766 " model vdw 2.226 3.040 nonbonded pdb=" O GLN B 35 " pdb=" OG SER B 39 " model vdw 2.244 3.040 nonbonded pdb=" OG SER C 657 " pdb=" OE1 GLN C 659 " model vdw 2.249 3.040 nonbonded pdb=" O TYR C1167 " pdb=" OG1 THR C1170 " model vdw 2.252 3.040 ... (remaining 153919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.580 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 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 : 0.010 0.270 17300 Z= 0.436 Angle : 1.305 31.561 23435 Z= 0.664 Chirality : 0.066 0.615 2662 Planarity : 0.009 0.089 3022 Dihedral : 11.428 120.717 6530 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.32 % Allowed : 3.46 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -4.57 (0.15), residues: 2123 helix: -2.81 (0.14), residues: 682 sheet: -2.76 (0.21), residues: 445 loop : -3.28 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 268 TYR 0.030 0.004 TYR C 623 PHE 0.047 0.004 PHE A 261 TRP 0.014 0.003 TRP C1055 HIS 0.014 0.003 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00862 (17290) covalent geometry : angle 1.27165 (23429) hydrogen bonds : bond 0.17987 ( 661) hydrogen bonds : angle 10.64236 ( 1878) metal coordination : bond 0.19959 ( 10) metal coordination : angle 18.22826 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 562 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.8025 (tp) cc_final: 0.7743 (tt) REVERT: B 38 ASP cc_start: 0.7279 (p0) cc_final: 0.7033 (p0) REVERT: B 64 VAL cc_start: 0.7069 (t) cc_final: 0.6701 (t) REVERT: C 773 LEU cc_start: 0.6651 (tp) cc_final: 0.6338 (mp) REVERT: C 933 CYS cc_start: 0.6350 (m) cc_final: 0.4982 (t) REVERT: A 222 ARG cc_start: 0.5751 (mtt180) cc_final: 0.5485 (ttm110) REVERT: A 891 VAL cc_start: 0.3520 (p) cc_final: 0.2030 (t) outliers start: 6 outliers final: 2 residues processed: 566 average time/residue: 0.1598 time to fit residues: 129.8013 Evaluate side-chains 322 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain A residue 948 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 46 HIS C 662 HIS C 692 HIS C 821 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 ASN C1142 ASN ** C1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN A 161 HIS A 194 ASN A 206 GLN A 231 HIS A 293 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 518 GLN A 636 GLN A 726 GLN A 775 ASN A 916 ASN A1061 ASN A1160 HIS A1181 GLN A1192 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.152196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.121813 restraints weight = 44791.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.125238 restraints weight = 25788.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.126486 restraints weight = 15376.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.127514 restraints weight = 11564.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.127865 restraints weight = 9525.988| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17300 Z= 0.156 Angle : 0.785 10.570 23435 Z= 0.396 Chirality : 0.047 0.223 2662 Planarity : 0.006 0.069 3022 Dihedral : 7.064 51.688 2420 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.46 % Allowed : 12.37 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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 aren not related in a simple way. whole: -3.25 (0.16), residues: 2123 helix: -1.06 (0.18), residues: 703 sheet: -2.25 (0.23), residues: 448 loop : -2.94 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 390 TYR 0.025 0.002 TYR C 830 PHE 0.031 0.002 PHE C 777 TRP 0.014 0.002 TRP A 536 HIS 0.006 0.001 HIS A1152 Details of bonding type rmsd covalent geometry : bond 0.00321 (17290) covalent geometry : angle 0.78253 (23429) hydrogen bonds : bond 0.04715 ( 661) hydrogen bonds : angle 6.54073 ( 1878) metal coordination : bond 0.00614 ( 10) metal coordination : angle 3.66288 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 371 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 587 TYR cc_start: 0.7127 (t80) cc_final: 0.6914 (t80) REVERT: C 675 MET cc_start: 0.6126 (ttm) cc_final: 0.5818 (ttm) REVERT: C 721 ILE cc_start: 0.5126 (OUTLIER) cc_final: 0.4674 (mt) REVERT: C 757 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7128 (ttp) REVERT: C 831 ARG cc_start: 0.7196 (ptt-90) cc_final: 0.6902 (ptt90) REVERT: C 933 CYS cc_start: 0.7593 (m) cc_final: 0.6329 (t) REVERT: C 1045 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6214 (mtm110) REVERT: C 1066 LEU cc_start: 0.6739 (mt) cc_final: 0.6238 (mp) REVERT: C 1260 LYS cc_start: 0.8792 (mppt) cc_final: 0.8568 (mppt) REVERT: D 10 PHE cc_start: 0.6942 (m-80) cc_final: 0.6722 (m-10) REVERT: A 120 PHE cc_start: 0.5940 (m-80) cc_final: 0.5438 (m-80) REVERT: A 133 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (m) REVERT: A 321 MET cc_start: 0.5840 (mmt) cc_final: 0.5555 (mmm) REVERT: A 447 MET cc_start: 0.2380 (mmm) cc_final: 0.2128 (mmm) REVERT: A 706 MET cc_start: 0.0787 (tmm) cc_final: 0.0333 (tpt) REVERT: A 1029 TYR cc_start: 0.6211 (m-10) cc_final: 0.5912 (m-80) REVERT: A 1093 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4785 (mmm) REVERT: A 1173 VAL cc_start: 0.7802 (t) cc_final: 0.7334 (t) outliers start: 64 outliers final: 28 residues processed: 410 average time/residue: 0.1292 time to fit residues: 80.2857 Evaluate side-chains 328 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 912 ASN Chi-restraints excluded: chain C residue 1045 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 208 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 46 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1184 HIS A 119 GLN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 818 GLN A1052 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.151246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.118488 restraints weight = 45344.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121480 restraints weight = 25804.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.123603 restraints weight = 17438.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.124909 restraints weight = 13202.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.125667 restraints weight = 10909.617| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17300 Z= 0.150 Angle : 0.736 10.690 23435 Z= 0.371 Chirality : 0.047 0.216 2662 Planarity : 0.005 0.065 3022 Dihedral : 6.147 69.739 2418 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.03 % Allowed : 15.29 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.53 (0.17), residues: 2123 helix: -0.22 (0.19), residues: 700 sheet: -1.91 (0.23), residues: 456 loop : -2.68 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1045 TYR 0.019 0.002 TYR A 224 PHE 0.029 0.001 PHE C1155 TRP 0.011 0.002 TRP C 732 HIS 0.029 0.001 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00326 (17290) covalent geometry : angle 0.73502 (23429) hydrogen bonds : bond 0.04297 ( 661) hydrogen bonds : angle 5.97353 ( 1878) metal coordination : bond 0.00426 ( 10) metal coordination : angle 2.96682 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 325 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.6229 (pt0) cc_final: 0.5900 (pm20) REVERT: C 532 PHE cc_start: 0.6941 (m-80) cc_final: 0.6361 (p90) REVERT: C 592 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6414 (mm-30) REVERT: C 675 MET cc_start: 0.6264 (ttm) cc_final: 0.5914 (ttm) REVERT: C 748 LYS cc_start: 0.7582 (tppt) cc_final: 0.7381 (tppt) REVERT: C 770 MET cc_start: 0.6283 (tmm) cc_final: 0.6054 (ppp) REVERT: C 832 GLN cc_start: 0.8024 (pt0) cc_final: 0.7720 (pp30) REVERT: C 932 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 948 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7808 (mmt90) REVERT: C 1009 MET cc_start: 0.7435 (tpp) cc_final: 0.6855 (mmm) REVERT: C 1260 LYS cc_start: 0.8907 (mppt) cc_final: 0.8659 (mppt) REVERT: D 24 GLU cc_start: 0.7136 (pm20) cc_final: 0.6895 (tp30) REVERT: A 221 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 321 MET cc_start: 0.5891 (mmt) cc_final: 0.5279 (mmm) REVERT: A 414 ASP cc_start: 0.8250 (t0) cc_final: 0.7960 (t0) REVERT: A 447 MET cc_start: 0.2413 (mmm) cc_final: 0.2205 (mmm) REVERT: A 706 MET cc_start: 0.0515 (tmm) cc_final: 0.0241 (tpt) REVERT: A 1029 TYR cc_start: 0.6419 (m-10) cc_final: 0.6170 (m-80) REVERT: A 1185 MET cc_start: 0.6231 (mmm) cc_final: 0.5948 (tpp) outliers start: 56 outliers final: 33 residues processed: 360 average time/residue: 0.1220 time to fit residues: 67.4833 Evaluate side-chains 328 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 852 ARG Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 948 ARG Chi-restraints excluded: chain C residue 1001 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1160 GLU Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 8 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 114 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 36 HIS B 46 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS ** C1283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 HIS A 818 GLN A 885 ASN A1152 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.151600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120765 restraints weight = 45197.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.123812 restraints weight = 27995.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.124876 restraints weight = 17624.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.126196 restraints weight = 13145.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.126399 restraints weight = 10640.425| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17300 Z= 0.138 Angle : 0.702 11.918 23435 Z= 0.351 Chirality : 0.046 0.277 2662 Planarity : 0.005 0.058 3022 Dihedral : 5.748 64.819 2418 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.21 % Allowed : 15.94 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.27 (0.18), residues: 2123 helix: -0.03 (0.20), residues: 707 sheet: -1.87 (0.22), residues: 473 loop : -2.46 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 614 TYR 0.013 0.001 TYR C 864 PHE 0.027 0.001 PHE C1155 TRP 0.012 0.001 TRP B 29 HIS 0.005 0.001 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00304 (17290) covalent geometry : angle 0.70111 (23429) hydrogen bonds : bond 0.03975 ( 661) hydrogen bonds : angle 5.63821 ( 1878) metal coordination : bond 0.00338 ( 10) metal coordination : angle 2.68684 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 313 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6098 (m90) REVERT: C 544 LEU cc_start: 0.8017 (tp) cc_final: 0.7517 (tp) REVERT: C 675 MET cc_start: 0.6489 (ttm) cc_final: 0.6068 (ttm) REVERT: C 721 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.4891 (mt) REVERT: C 748 LYS cc_start: 0.7694 (tppt) cc_final: 0.7493 (tppt) REVERT: C 770 MET cc_start: 0.6326 (tmm) cc_final: 0.6080 (ppp) REVERT: C 832 GLN cc_start: 0.8071 (pt0) cc_final: 0.7723 (pp30) REVERT: C 876 MET cc_start: 0.6843 (mpp) cc_final: 0.6401 (mmp) REVERT: C 932 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8787 (tp) REVERT: C 1155 PHE cc_start: 0.7891 (m-80) cc_final: 0.7544 (m-80) REVERT: D 24 GLU cc_start: 0.7252 (pm20) cc_final: 0.6956 (mm-30) REVERT: A 110 SER cc_start: 0.7188 (OUTLIER) cc_final: 0.6881 (t) REVERT: A 309 ASP cc_start: 0.5582 (m-30) cc_final: 0.5326 (m-30) REVERT: A 321 MET cc_start: 0.6082 (mmt) cc_final: 0.5568 (mmm) REVERT: A 414 ASP cc_start: 0.8276 (t0) cc_final: 0.8004 (t0) REVERT: A 447 MET cc_start: 0.2407 (mmm) cc_final: 0.2160 (mmm) REVERT: A 706 MET cc_start: 0.0517 (tmm) cc_final: 0.0283 (tpt) REVERT: A 783 TYR cc_start: 0.7727 (m-10) cc_final: 0.7228 (m-10) REVERT: A 849 GLU cc_start: 0.7772 (tt0) cc_final: 0.7567 (tp30) REVERT: A 1029 TYR cc_start: 0.6669 (m-10) cc_final: 0.6413 (m-80) REVERT: A 1093 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5392 (tpp) outliers start: 78 outliers final: 43 residues processed: 362 average time/residue: 0.1211 time to fit residues: 67.5283 Evaluate side-chains 324 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 852 ARG Chi-restraints excluded: chain C residue 875 ILE Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 97 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 36 HIS B 46 HIS C 599 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 886 HIS C1283 HIS ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 356 HIS A 666 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.118290 restraints weight = 45585.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.120408 restraints weight = 25610.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.121524 restraints weight = 17354.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.122254 restraints weight = 13436.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.122475 restraints weight = 11560.723| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17300 Z= 0.168 Angle : 0.741 12.787 23435 Z= 0.376 Chirality : 0.047 0.197 2662 Planarity : 0.005 0.060 3022 Dihedral : 5.713 62.816 2418 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.05 % Allowed : 17.02 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.20 (0.18), residues: 2123 helix: -0.04 (0.19), residues: 716 sheet: -1.76 (0.23), residues: 452 loop : -2.41 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 822 TYR 0.019 0.002 TYR C 864 PHE 0.020 0.002 PHE C1155 TRP 0.014 0.002 TRP B 31 HIS 0.073 0.002 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00379 (17290) covalent geometry : angle 0.73928 (23429) hydrogen bonds : bond 0.04221 ( 661) hydrogen bonds : angle 5.58334 ( 1878) metal coordination : bond 0.00538 ( 10) metal coordination : angle 3.51026 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 297 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 544 LEU cc_start: 0.7819 (tp) cc_final: 0.7460 (tp) REVERT: C 662 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7867 (t-90) REVERT: C 675 MET cc_start: 0.6593 (ttm) cc_final: 0.6110 (ttm) REVERT: C 721 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5095 (mt) REVERT: C 757 MET cc_start: 0.7588 (tpp) cc_final: 0.7237 (ttt) REVERT: C 832 GLN cc_start: 0.8193 (pt0) cc_final: 0.7866 (pm20) REVERT: C 932 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8840 (tp) REVERT: C 1014 LYS cc_start: 0.6308 (mptt) cc_final: 0.6034 (tppt) REVERT: C 1205 GLU cc_start: 0.4872 (mp0) cc_final: 0.4540 (mp0) REVERT: C 1216 TRP cc_start: 0.7763 (t-100) cc_final: 0.7310 (t60) REVERT: C 1222 THR cc_start: 0.8121 (p) cc_final: 0.7840 (p) REVERT: D 24 GLU cc_start: 0.7248 (pm20) cc_final: 0.6941 (mm-30) REVERT: D 79 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: A 39 GLU cc_start: 0.7836 (tt0) cc_final: 0.7260 (tm-30) REVERT: A 110 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7610 (t) REVERT: A 166 LEU cc_start: 0.8670 (mt) cc_final: 0.8462 (tp) REVERT: A 321 MET cc_start: 0.5967 (mmt) cc_final: 0.5476 (mmm) REVERT: A 447 MET cc_start: 0.2326 (mmm) cc_final: 0.2046 (mmm) REVERT: A 1017 ASN cc_start: 0.8389 (p0) cc_final: 0.8053 (p0) REVERT: A 1029 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: A 1146 MET cc_start: 0.8080 (ppp) cc_final: 0.7863 (ppp) outliers start: 75 outliers final: 39 residues processed: 340 average time/residue: 0.1216 time to fit residues: 64.6649 Evaluate side-chains 316 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 662 HIS Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 209 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS A 119 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 HIS ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.147439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116517 restraints weight = 45883.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.118678 restraints weight = 29100.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119685 restraints weight = 20201.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.120731 restraints weight = 14338.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.121063 restraints weight = 11714.995| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.7547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17300 Z= 0.143 Angle : 0.716 10.869 23435 Z= 0.354 Chirality : 0.047 0.323 2662 Planarity : 0.005 0.057 3022 Dihedral : 5.491 64.348 2418 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.40 % Allowed : 19.02 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.03 (0.18), residues: 2123 helix: 0.05 (0.19), residues: 719 sheet: -1.49 (0.24), residues: 438 loop : -2.37 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 390 TYR 0.013 0.001 TYR C 864 PHE 0.011 0.001 PHE A 939 TRP 0.013 0.001 TRP B 29 HIS 0.017 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00331 (17290) covalent geometry : angle 0.71398 (23429) hydrogen bonds : bond 0.03851 ( 661) hydrogen bonds : angle 5.44200 ( 1878) metal coordination : bond 0.00421 ( 10) metal coordination : angle 3.67226 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 301 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 544 LEU cc_start: 0.7556 (tp) cc_final: 0.7117 (tp) REVERT: C 662 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7357 (t-90) REVERT: C 675 MET cc_start: 0.6607 (ttm) cc_final: 0.6060 (ttm) REVERT: C 770 MET cc_start: 0.5874 (ppp) cc_final: 0.5464 (ptt) REVERT: C 835 ASP cc_start: 0.7449 (m-30) cc_final: 0.7193 (m-30) REVERT: C 867 MET cc_start: 0.8487 (ptp) cc_final: 0.8008 (ttt) REVERT: C 898 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.5095 (t80) REVERT: C 933 CYS cc_start: 0.7435 (m) cc_final: 0.6716 (t) REVERT: C 1014 LYS cc_start: 0.6889 (mptt) cc_final: 0.6441 (tptp) REVERT: C 1269 TYR cc_start: 0.7198 (t80) cc_final: 0.6899 (t80) REVERT: D 24 GLU cc_start: 0.7348 (pm20) cc_final: 0.7114 (mm-30) REVERT: D 79 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: A 39 GLU cc_start: 0.7843 (tt0) cc_final: 0.7366 (tm-30) REVERT: A 140 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 321 MET cc_start: 0.6394 (mmt) cc_final: 0.6146 (mmm) REVERT: A 447 MET cc_start: 0.2271 (mmm) cc_final: 0.2012 (mmm) REVERT: A 889 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: A 1017 ASN cc_start: 0.8524 (p0) cc_final: 0.8237 (p0) REVERT: A 1029 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6972 (m-10) outliers start: 63 outliers final: 40 residues processed: 332 average time/residue: 0.1171 time to fit residues: 60.9660 Evaluate side-chains 305 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 662 HIS Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1069 HIS Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 119 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 ASN ** A1087 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 = 0.4280 r_free = 0.4280 target = 0.146535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116314 restraints weight = 45640.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.119033 restraints weight = 26970.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119820 restraints weight = 17138.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.120498 restraints weight = 14127.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.120860 restraints weight = 11805.495| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.8194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17300 Z= 0.150 Angle : 0.748 16.898 23435 Z= 0.369 Chirality : 0.047 0.235 2662 Planarity : 0.005 0.057 3022 Dihedral : 5.541 63.700 2418 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.30 % Allowed : 19.34 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.00 (0.18), residues: 2123 helix: 0.01 (0.19), residues: 720 sheet: -1.46 (0.24), residues: 451 loop : -2.30 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 948 TYR 0.014 0.001 TYR A1215 PHE 0.011 0.001 PHE C 777 TRP 0.029 0.002 TRP C1216 HIS 0.007 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00350 (17290) covalent geometry : angle 0.74629 (23429) hydrogen bonds : bond 0.03886 ( 661) hydrogen bonds : angle 5.45990 ( 1878) metal coordination : bond 0.00472 ( 10) metal coordination : angle 3.18753 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8669 (m-30) REVERT: C 545 GLU cc_start: 0.8570 (tp30) cc_final: 0.8229 (tp30) REVERT: C 662 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7380 (t-90) REVERT: C 675 MET cc_start: 0.6554 (ttm) cc_final: 0.6075 (ttm) REVERT: C 770 MET cc_start: 0.5829 (ppp) cc_final: 0.5441 (ptt) REVERT: C 898 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.5153 (t80) REVERT: C 933 CYS cc_start: 0.7587 (m) cc_final: 0.6504 (t) REVERT: C 1014 LYS cc_start: 0.6913 (mptt) cc_final: 0.6648 (tptt) REVERT: C 1037 ASP cc_start: 0.7706 (m-30) cc_final: 0.7483 (m-30) REVERT: D 24 GLU cc_start: 0.7297 (pm20) cc_final: 0.7092 (mm-30) REVERT: D 48 GLU cc_start: 0.8324 (mp0) cc_final: 0.8040 (pm20) REVERT: D 71 TYR cc_start: 0.7756 (m-80) cc_final: 0.7392 (m-10) REVERT: D 79 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: A 39 GLU cc_start: 0.7877 (tt0) cc_final: 0.7483 (tm-30) REVERT: A 66 MET cc_start: 0.5748 (ttm) cc_final: 0.5352 (ttp) REVERT: A 140 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 321 MET cc_start: 0.6688 (mmt) cc_final: 0.6057 (mmm) REVERT: A 447 MET cc_start: 0.2179 (mmm) cc_final: 0.1937 (mmm) REVERT: A 889 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: A 1017 ASN cc_start: 0.8613 (p0) cc_final: 0.8400 (p0) REVERT: A 1146 MET cc_start: 0.8183 (ppp) cc_final: 0.7966 (ppp) outliers start: 61 outliers final: 39 residues processed: 307 average time/residue: 0.1204 time to fit residues: 58.7234 Evaluate side-chains 298 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 662 HIS Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1069 HIS Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain C residue 1246 MET Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 125 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 162 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 157 optimal weight: 30.0000 chunk 208 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.143629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.114241 restraints weight = 47431.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.114502 restraints weight = 28536.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115635 restraints weight = 22221.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.115854 restraints weight = 17076.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.116052 restraints weight = 15569.627| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.9189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17300 Z= 0.184 Angle : 0.801 12.647 23435 Z= 0.398 Chirality : 0.049 0.266 2662 Planarity : 0.005 0.056 3022 Dihedral : 5.734 64.122 2418 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.67 % Allowed : 20.15 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.16 (0.17), residues: 2123 helix: -0.19 (0.19), residues: 720 sheet: -1.53 (0.24), residues: 444 loop : -2.35 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 222 TYR 0.017 0.002 TYR C 752 PHE 0.013 0.002 PHE C 777 TRP 0.039 0.002 TRP C1216 HIS 0.009 0.002 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00429 (17290) covalent geometry : angle 0.79911 (23429) hydrogen bonds : bond 0.04446 ( 661) hydrogen bonds : angle 5.61324 ( 1878) metal coordination : bond 0.00490 ( 10) metal coordination : angle 3.06157 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 545 GLU cc_start: 0.8739 (tp30) cc_final: 0.8484 (tp30) REVERT: C 662 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: C 675 MET cc_start: 0.6421 (ttm) cc_final: 0.6001 (ttm) REVERT: C 770 MET cc_start: 0.5968 (ppp) cc_final: 0.5624 (ptt) REVERT: C 823 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.3554 (mmm) REVERT: C 832 GLN cc_start: 0.8605 (pt0) cc_final: 0.8302 (pm20) REVERT: C 898 TYR cc_start: 0.5793 (OUTLIER) cc_final: 0.4698 (t80) REVERT: C 918 VAL cc_start: 0.8512 (t) cc_final: 0.8264 (m) REVERT: C 933 CYS cc_start: 0.7743 (m) cc_final: 0.6589 (t) REVERT: D 35 SER cc_start: 0.9076 (t) cc_final: 0.8661 (p) REVERT: D 79 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: A 1 MET cc_start: 0.6402 (ttt) cc_final: 0.4923 (tpt) REVERT: A 321 MET cc_start: 0.6329 (mmt) cc_final: 0.5720 (mmm) REVERT: A 360 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: A 447 MET cc_start: 0.1943 (mmm) cc_final: 0.1743 (mmm) REVERT: A 883 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: A 889 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: A 1017 ASN cc_start: 0.8728 (p0) cc_final: 0.8372 (p0) REVERT: A 1146 MET cc_start: 0.8044 (ppp) cc_final: 0.7750 (ppp) outliers start: 68 outliers final: 46 residues processed: 315 average time/residue: 0.1205 time to fit residues: 59.3321 Evaluate side-chains 291 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 662 HIS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain C residue 1246 MET Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1138 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 74 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1194 HIS A 254 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.146633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.115837 restraints weight = 46435.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.117436 restraints weight = 29412.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.118534 restraints weight = 20619.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.119773 restraints weight = 15331.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119919 restraints weight = 12558.840| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17300 Z= 0.132 Angle : 0.774 12.852 23435 Z= 0.377 Chirality : 0.047 0.238 2662 Planarity : 0.005 0.058 3022 Dihedral : 5.529 64.627 2418 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.86 % Allowed : 21.99 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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 aren not related in a simple way. whole: -1.94 (0.18), residues: 2123 helix: 0.04 (0.19), residues: 719 sheet: -1.41 (0.24), residues: 473 loop : -2.27 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 222 TYR 0.018 0.001 TYR C1249 PHE 0.010 0.001 PHE A1217 TRP 0.053 0.002 TRP C1216 HIS 0.007 0.001 HIS C 662 Details of bonding type rmsd covalent geometry : bond 0.00302 (17290) covalent geometry : angle 0.77297 (23429) hydrogen bonds : bond 0.03973 ( 661) hydrogen bonds : angle 5.41806 ( 1878) metal coordination : bond 0.00228 ( 10) metal coordination : angle 3.12809 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 545 GLU cc_start: 0.8678 (tp30) cc_final: 0.8392 (tp30) REVERT: C 662 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8043 (t-90) REVERT: C 675 MET cc_start: 0.6305 (ttm) cc_final: 0.5945 (ttm) REVERT: C 770 MET cc_start: 0.6121 (ppp) cc_final: 0.5810 (ptt) REVERT: C 823 MET cc_start: 0.4160 (OUTLIER) cc_final: 0.3578 (mmm) REVERT: C 864 TYR cc_start: 0.7611 (t80) cc_final: 0.7287 (t80) REVERT: C 867 MET cc_start: 0.8387 (ptp) cc_final: 0.7882 (ttt) REVERT: C 876 MET cc_start: 0.6153 (mmp) cc_final: 0.5504 (mmp) REVERT: C 898 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.4711 (t80) REVERT: C 918 VAL cc_start: 0.8521 (t) cc_final: 0.8254 (m) REVERT: C 933 CYS cc_start: 0.7816 (m) cc_final: 0.6703 (t) REVERT: C 1133 MET cc_start: 0.7254 (mmp) cc_final: 0.6886 (mmp) REVERT: D 35 SER cc_start: 0.9032 (t) cc_final: 0.8672 (p) REVERT: D 78 GLN cc_start: 0.8597 (tt0) cc_final: 0.8303 (tt0) REVERT: D 79 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: A 1 MET cc_start: 0.6358 (ttt) cc_final: 0.5023 (tpt) REVERT: A 199 GLU cc_start: 0.7044 (tp30) cc_final: 0.6253 (pp20) REVERT: A 321 MET cc_start: 0.6141 (mmt) cc_final: 0.5602 (mmm) REVERT: A 883 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 889 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: A 1017 ASN cc_start: 0.8489 (p0) cc_final: 0.8039 (p0) REVERT: A 1146 MET cc_start: 0.8276 (ppp) cc_final: 0.8071 (ppp) outliers start: 53 outliers final: 35 residues processed: 299 average time/residue: 0.1009 time to fit residues: 47.7471 Evaluate side-chains 291 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 662 HIS Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1138 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 117 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 chunk 109 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 165 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 861 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.147915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.118153 restraints weight = 45143.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.120018 restraints weight = 25833.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121168 restraints weight = 17599.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.121936 restraints weight = 13430.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121987 restraints weight = 11640.962| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.9551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17300 Z= 0.129 Angle : 0.783 12.899 23435 Z= 0.381 Chirality : 0.047 0.298 2662 Planarity : 0.004 0.056 3022 Dihedral : 5.422 64.934 2418 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.16 % Allowed : 23.55 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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 aren not related in a simple way. whole: -1.83 (0.18), residues: 2123 helix: 0.07 (0.19), residues: 721 sheet: -1.27 (0.24), residues: 472 loop : -2.20 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 222 TYR 0.014 0.001 TYR C1249 PHE 0.047 0.001 PHE A 59 TRP 0.045 0.002 TRP C1216 HIS 0.008 0.001 HIS C 662 Details of bonding type rmsd covalent geometry : bond 0.00297 (17290) covalent geometry : angle 0.78210 (23429) hydrogen bonds : bond 0.03875 ( 661) hydrogen bonds : angle 5.31507 ( 1878) metal coordination : bond 0.00215 ( 10) metal coordination : angle 2.65887 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 545 GLU cc_start: 0.8696 (tp30) cc_final: 0.8407 (tp30) REVERT: C 662 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.8083 (t-90) REVERT: C 675 MET cc_start: 0.6350 (ttm) cc_final: 0.6141 (ttm) REVERT: C 679 ILE cc_start: 0.8104 (mt) cc_final: 0.7630 (mt) REVERT: C 719 TYR cc_start: 0.5265 (OUTLIER) cc_final: 0.4892 (m-80) REVERT: C 770 MET cc_start: 0.6100 (ppp) cc_final: 0.5750 (ptt) REVERT: C 823 MET cc_start: 0.3959 (OUTLIER) cc_final: 0.3427 (mmm) REVERT: C 835 ASP cc_start: 0.7758 (m-30) cc_final: 0.7550 (m-30) REVERT: C 864 TYR cc_start: 0.7467 (t80) cc_final: 0.7205 (t80) REVERT: C 867 MET cc_start: 0.8492 (ptp) cc_final: 0.8015 (ttt) REVERT: C 876 MET cc_start: 0.5857 (mmp) cc_final: 0.5190 (mmp) REVERT: C 898 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.4872 (t80) REVERT: C 933 CYS cc_start: 0.7836 (m) cc_final: 0.6747 (t) REVERT: C 1036 ILE cc_start: 0.8664 (mt) cc_final: 0.8424 (mm) REVERT: C 1133 MET cc_start: 0.7283 (mmp) cc_final: 0.6848 (mmp) REVERT: D 13 LYS cc_start: 0.8880 (ptmm) cc_final: 0.8623 (tmtt) REVERT: D 35 SER cc_start: 0.9005 (t) cc_final: 0.8625 (p) REVERT: D 78 GLN cc_start: 0.8574 (tt0) cc_final: 0.8303 (tt0) REVERT: D 79 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: A 1 MET cc_start: 0.6170 (ttt) cc_final: 0.4962 (tpt) REVERT: A 199 GLU cc_start: 0.7069 (tp30) cc_final: 0.6620 (pt0) REVERT: A 321 MET cc_start: 0.6124 (mmt) cc_final: 0.5636 (mmm) REVERT: A 883 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: A 889 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: A 1017 ASN cc_start: 0.8546 (p0) cc_final: 0.8063 (p0) outliers start: 40 outliers final: 28 residues processed: 284 average time/residue: 0.1000 time to fit residues: 45.1851 Evaluate side-chains 283 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 662 HIS Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 719 TYR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1138 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 128 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 795 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.146456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.117117 restraints weight = 46670.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.117770 restraints weight = 26109.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118826 restraints weight = 19773.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.119393 restraints weight = 15899.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.120522 restraints weight = 14338.729| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.9806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17300 Z= 0.137 Angle : 0.779 15.459 23435 Z= 0.380 Chirality : 0.047 0.215 2662 Planarity : 0.004 0.057 3022 Dihedral : 5.433 65.051 2418 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.22 % Allowed : 23.77 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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 aren not related in a simple way. whole: -1.84 (0.18), residues: 2123 helix: 0.06 (0.20), residues: 717 sheet: -1.27 (0.24), residues: 461 loop : -2.19 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.012 0.001 TYR A 224 PHE 0.012 0.001 PHE A 59 TRP 0.041 0.002 TRP C1216 HIS 0.006 0.001 HIS C 662 Details of bonding type rmsd covalent geometry : bond 0.00322 (17290) covalent geometry : angle 0.77799 (23429) hydrogen bonds : bond 0.03863 ( 661) hydrogen bonds : angle 5.29011 ( 1878) metal coordination : bond 0.00279 ( 10) metal coordination : angle 2.58809 ( 6) =============================================================================== Job complete usr+sys time: 2818.91 seconds wall clock time: 49 minutes 28.56 seconds (2968.56 seconds total)