Starting phenix.real_space_refine on Sun Sep 13 04:38:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q3l_13793/09_2026/7q3l_13793.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 41 5.49 5 S 116 5.16 5 C 12767 2.51 5 N 3487 2.21 5 O 4055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20470 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 940 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain breaks: 3 Chain: "C" Number of atoms: 9336 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1189, 9328 Classifications: {'peptide': 1189} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1189, 9328 Classifications: {'peptide': 1189} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 5 bond proxies already assigned to first conformer: 9511 Chain: "E" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 575 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "G" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 613 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "2" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 865 Classifications: {'RNAv2': 41} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 21} Link IDs: {'rna2p': 1, 'rna3p': 39} Chain breaks: 1 Chain: "9" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 769 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "q" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain breaks: 4 Chain: "A" Number of atoms: 6479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6479 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 779} Chain: "p" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 172 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" 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: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11014 SG CYS G 30 53.808 76.139 54.293 1.00 46.00 S ATOM 11035 SG CYS G 33 51.977 73.925 51.986 1.00 53.12 S ATOM 11330 SG CYS G 72 51.373 73.370 55.474 1.00 37.12 S ATOM 11354 SG CYS G 75 54.758 72.631 54.919 1.00 39.31 S ATOM 10876 SG CYS G 11 68.714 82.034 54.388 1.00 61.87 S ATOM 11139 SG CYS G 46 68.971 84.628 57.331 1.00 54.35 S ATOM 11162 SG CYS G 49 67.656 85.519 54.357 1.00 74.46 S ATOM 11433 SG CYS G 85 65.890 82.959 56.489 1.00 48.28 S ATOM 10963 SG CYS G 23 53.584 89.393 48.327 1.00 60.94 S ATOM 10987 SG CYS G 26 53.366 85.852 47.148 1.00 69.47 S ATOM 11234 SG CYS G 58 56.163 87.542 49.954 1.00 74.06 S ATOM 11255 SG CYS G 61 56.589 88.752 46.474 1.00 71.13 S ATOM 12479 SG CYS 9 408 70.855 24.125 34.333 1.00211.34 S ATOM 12502 SG CYS 9 411 68.026 23.230 32.560 1.00211.34 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET C 1 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET C 1 " occ=0.50 Time building chain proxies: 5.33, per 1000 atoms: 0.26 Number of scatterers: 20470 At special positions: 0 Unit cell: (116.48, 138.88, 147.2, 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 4 29.99 S 116 16.00 P 41 15.00 O 4055 8.00 N 3487 7.00 C 12767 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: 1.68 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 9 601 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 408 " pdb="ZN ZN 9 601 " - pdb=" ND1 HIS 9 431 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 411 " pdb="ZN ZN 9 601 " - pdb=" ND1 HIS 9 425 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 72 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 75 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 30 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 85 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 11 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 49 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 46 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 23 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 61 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 58 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 26 " Number of angles added : 20 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4580 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 28 sheets defined 44.8% alpha, 21.3% beta 10 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.504A pdb=" N MET B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.713A pdb=" N VAL B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 476 through 482 removed outlier: 3.860A pdb=" N VAL B 480 " --> pdb=" O MET B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.171A pdb=" N CYS B 505 " --> pdb=" O ARG B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.975A pdb=" N PHE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 429 through 432 Processing helix chain 'C' and resid 808 through 825 Processing helix chain 'C' and resid 832 through 845 Processing helix chain 'C' and resid 848 through 853 Processing helix chain 'C' and resid 1072 through 1076 Processing helix chain 'C' and resid 1134 through 1152 removed outlier: 4.576A pdb=" N PHE C1140 " --> pdb=" O GLU C1136 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C1150 " --> pdb=" O MET C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1165 Processing helix chain 'C' and resid 1176 through 1180 Processing helix chain 'C' and resid 1181 through 1185 Processing helix chain 'C' and resid 1186 through 1196 Processing helix chain 'C' and resid 1200 through 1216 removed outlier: 3.909A pdb=" N TYR C1215 " --> pdb=" O ILE C1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'E' and resid 27 through 46 Processing helix chain 'E' and resid 46 through 58 Processing helix chain 'E' and resid 60 through 72 Processing helix chain 'G' and resid 47 through 55 removed outlier: 3.549A pdb=" N TYR G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLY G 52 " --> pdb=" O CYS G 49 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER G 53 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.881A pdb=" N ASP G 83 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain '9' and resid 394 through 399 Processing helix chain '9' and resid 418 through 423 Processing helix chain '9' and resid 424 through 427 Processing helix chain '9' and resid 428 through 438 Processing helix chain '9' and resid 443 through 447 Processing helix chain '9' and resid 451 through 469 Processing helix chain '9' and resid 472 through 476 Processing helix chain 'q' and resid 146 through 155 removed outlier: 3.600A pdb=" N GLN q 151 " --> pdb=" O ASP q 147 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS q 155 " --> pdb=" O GLN q 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 191 through 201 removed outlier: 3.882A pdb=" N GLU q 195 " --> pdb=" O ARG q 191 " (cutoff:3.500A) Processing helix chain 'q' and resid 241 through 245 Processing helix chain 'A' and resid 492 through 506 Processing helix chain 'A' and resid 508 through 527 removed outlier: 4.942A pdb=" N ARG A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLU A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 Proline residue: A 537 - end of helix Processing helix chain 'A' and resid 545 through 564 removed outlier: 4.267A pdb=" N ARG A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.752A pdb=" N VAL A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 605 through 618 Proline residue: A 615 - end of helix removed outlier: 3.954A pdb=" N ASP A 618 " --> pdb=" O ARG A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.786A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 657 through 676 Processing helix chain 'A' and resid 677 through 681 Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 682 through 691 removed outlier: 3.517A pdb=" N ILE A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 698 through 717 Processing helix chain 'A' and resid 720 through 736 removed outlier: 3.868A pdb=" N PHE A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 725 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL A 727 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Proline residue: A 730 - end of helix Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.927A pdb=" N PHE A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.698A pdb=" N LEU A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 798 Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 810 through 819 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.600A pdb=" N LEU A 825 " --> pdb=" O ARG A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 845 Processing helix chain 'A' and resid 845 through 854 removed outlier: 3.827A pdb=" N ILE A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 861 through 880 Processing helix chain 'A' and resid 885 through 903 removed outlier: 3.680A pdb=" N GLN A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 922 Processing helix chain 'A' and resid 923 through 927 Proline residue: A 927 - end of helix Processing helix chain 'A' and resid 928 through 941 Processing helix chain 'A' and resid 944 through 963 removed outlier: 5.746A pdb=" N VAL A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 982 removed outlier: 3.517A pdb=" N HIS A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1002 removed outlier: 3.639A pdb=" N SER A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 999 " --> pdb=" O GLY A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 Processing helix chain 'A' and resid 1012 through 1021 Proline residue: A1018 - end of helix Processing helix chain 'A' and resid 1022 through 1026 Processing helix chain 'A' and resid 1028 through 1046 Processing helix chain 'A' and resid 1047 through 1050 removed outlier: 3.828A pdb=" N VAL A1050 " --> pdb=" O ALA A1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1047 through 1050' Processing helix chain 'A' and resid 1051 through 1063 Processing helix chain 'A' and resid 1064 through 1068 Processing helix chain 'A' and resid 1070 through 1089 Processing helix chain 'A' and resid 1089 through 1101 removed outlier: 4.193A pdb=" N VAL A1093 " --> pdb=" O GLY A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1122 Processing helix chain 'A' and resid 1124 through 1127 Processing helix chain 'A' and resid 1128 through 1137 removed outlier: 3.522A pdb=" N ARG A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1159 Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 3.639A pdb=" N LYS A1163 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1179 Proline residue: A1171 - end of helix Processing helix chain 'A' and resid 1181 through 1200 Processing helix chain 'A' and resid 1204 through 1216 removed outlier: 3.865A pdb=" N TYR A1214 " --> pdb=" O HIS A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 removed outlier: 3.817A pdb=" N PHE A1220 " --> pdb=" O PRO A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1241 removed outlier: 4.114A pdb=" N VAL A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1251 removed outlier: 3.530A pdb=" N MET A1246 " --> pdb=" O GLY A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1258 through 1277 removed outlier: 3.871A pdb=" N VAL A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1284 removed outlier: 4.092A pdb=" N HIS A1283 " --> pdb=" O ALA A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 removed outlier: 3.670A pdb=" N ASP A1301 " --> pdb=" O ARG A1297 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 174 Processing sheet with id=AA1, first strand: chain 'C' and resid 1101 through 1107 removed outlier: 3.959A pdb=" N SER C1103 " --> pdb=" O THR C1120 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C1126 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 3 " --> pdb=" O ILE C1174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 20 removed outlier: 3.581A pdb=" N PHE C 16 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 38 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR C 55 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU C 40 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 68 removed outlier: 5.034A pdb=" N SER C 82 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 87 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN C 104 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 89 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 123 Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 123 Processing sheet with id=AA6, first strand: chain 'C' and resid 165 through 173 removed outlier: 6.588A pdb=" N LEU C 185 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL C 170 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA C 183 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLY C 172 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET C 181 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU C 212 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG C 222 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP C 214 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL C 220 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 232 through 237 removed outlier: 3.586A pdb=" N PHE C 234 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 274 removed outlier: 6.340A pdb=" N ARG C 273 " --> pdb=" O PHE C 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 287 through 295 removed outlier: 3.965A pdb=" N CYS C 289 " --> pdb=" O GLN C 304 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE C 299 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU C 315 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 331 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 312 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR C 329 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR C 314 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU C 327 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU C 316 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE C 325 " --> pdb=" O GLU C 316 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASP C 318 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR C 323 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 336 through 342 removed outlier: 3.717A pdb=" N PHE C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HIS C 356 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU C 400 " --> pdb=" O HIS C 356 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 358 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 413 removed outlier: 3.605A pdb=" N PHE C 409 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 445 through 450 removed outlier: 5.468A pdb=" N GLU C 446 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA C 766 " --> pdb=" O GLU C 446 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 458 through 462 removed outlier: 4.705A pdb=" N VAL C 484 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 507 through 510 Processing sheet with id=AB6, first strand: chain 'C' and resid 544 through 549 Processing sheet with id=AB7, first strand: chain 'C' and resid 544 through 549 removed outlier: 3.633A pdb=" N LYS C 581 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 587 through 592 removed outlier: 3.655A pdb=" N CYS C 589 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 629 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER C 618 " --> pdb=" O PRO C 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 637 through 643 removed outlier: 6.675A pdb=" N GLY C 668 " --> pdb=" O GLU C 638 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 640 " --> pdb=" O ASN C 666 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 666 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE C 642 " --> pdb=" O TYR C 664 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR C 664 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 700 through 706 removed outlier: 7.742A pdb=" N GLU C 710 " --> pdb=" O SER C 724 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER C 724 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 785 through 790 removed outlier: 6.375A pdb=" N THR C 802 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 787 " --> pdb=" O ILE C 800 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 886 through 895 removed outlier: 6.658A pdb=" N GLY C 908 " --> pdb=" O PHE C 889 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 891 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 906 " --> pdb=" O VAL C 891 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 893 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR C 904 " --> pdb=" O VAL C 893 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP C 903 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY C 923 " --> pdb=" O PRO C 944 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 925 " --> pdb=" O LYS C 942 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS C 942 " --> pdb=" O VAL C 925 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C 927 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 949 through 955 removed outlier: 3.743A pdb=" N ALA C 951 " --> pdb=" O GLY C 962 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 967 " --> pdb=" O GLU C 982 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 982 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 969 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 990 through 996 removed outlier: 6.656A pdb=" N SER C1003 " --> pdb=" O SER C 991 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE C 993 " --> pdb=" O ILE C1001 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C1001 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR C 995 " --> pdb=" O ARG C 999 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE C1009 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP C1026 " --> pdb=" O PHE C1009 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP C1011 " --> pdb=" O PHE C1024 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C1087 " --> pdb=" O PHE C1024 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1033 through 1040 removed outlier: 3.753A pdb=" N THR C1035 " --> pdb=" O ALA C1047 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C1043 " --> pdb=" O LEU C1039 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C1053 " --> pdb=" O ASN C1094 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN C1094 " --> pdb=" O ILE C1053 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C1055 " --> pdb=" O ILE C1092 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 21 through 22 Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 42 Processing sheet with id=AC9, first strand: chain '9' and resid 407 through 408 removed outlier: 3.637A pdb=" N TYR 9 414 " --> pdb=" O CYS 9 408 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'q' and resid 185 through 187 971 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3317 1.31 - 1.44: 5482 1.44 - 1.57: 11719 1.57 - 1.70: 81 1.70 - 1.83: 179 Bond restraints: 20778 Sorted by residual: bond pdb=" C CYS G 75 " pdb=" O CYS G 75 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.19e-02 7.06e+03 2.28e+01 bond pdb=" CA SER G 35 " pdb=" CB SER G 35 " ideal model delta sigma weight residual 1.529 1.458 0.072 1.64e-02 3.72e+03 1.91e+01 bond pdb=" C TYR G 71 " pdb=" O TYR G 71 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.22e-02 6.72e+03 1.88e+01 bond pdb=" C GLU G 74 " pdb=" O GLU G 74 " ideal model delta sigma weight residual 1.237 1.187 0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C SER A1051 " pdb=" N ALA A1052 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.31e-02 5.83e+03 1.39e+01 ... (remaining 20773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 26008 2.69 - 5.37: 2133 5.37 - 8.06: 162 8.06 - 10.75: 8 10.75 - 13.44: 1 Bond angle restraints: 28312 Sorted by residual: angle pdb=" CA ASP A1164 " pdb=" CB ASP A1164 " pdb=" CG ASP A1164 " ideal model delta sigma weight residual 112.60 120.12 -7.52 1.00e+00 1.00e+00 5.65e+01 angle pdb=" CA ASP C 419 " pdb=" CB ASP C 419 " pdb=" CG ASP C 419 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.40e+01 angle pdb=" C TYR 9 479 " pdb=" CA TYR 9 479 " pdb=" CB TYR 9 479 " ideal model delta sigma weight residual 109.68 123.12 -13.44 2.05e+00 2.38e-01 4.30e+01 angle pdb=" CA ASP C1064 " pdb=" CB ASP C1064 " pdb=" CG ASP C1064 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" N PRO G 39 " pdb=" CA PRO G 39 " pdb=" CB PRO G 39 " ideal model delta sigma weight residual 103.19 97.41 5.78 9.00e-01 1.23e+00 4.12e+01 ... (remaining 28307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.59: 11330 18.59 - 37.17: 838 37.17 - 55.76: 235 55.76 - 74.34: 57 74.34 - 92.93: 30 Dihedral angle restraints: 12490 sinusoidal: 5396 harmonic: 7094 Sorted by residual: dihedral pdb=" C4' C 2 45 " pdb=" C3' C 2 45 " pdb=" C2' C 2 45 " pdb=" C1' C 2 45 " ideal model delta sinusoidal sigma weight residual 36.34 -31.03 67.38 1 3.10e+00 1.04e-01 6.15e+02 dihedral pdb=" O4' C 2 45 " pdb=" C4' C 2 45 " pdb=" C3' C 2 45 " pdb=" C2' C 2 45 " ideal model delta sinusoidal sigma weight residual -35.15 18.73 -53.87 1 4.00e+00 6.25e-02 2.46e+02 dihedral pdb=" O4' C 2 45 " pdb=" C2' C 2 45 " pdb=" C1' C 2 45 " pdb=" C3' C 2 45 " ideal model delta sinusoidal sigma weight residual 25.59 -33.77 59.36 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 12487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2720 0.161 - 0.322: 422 0.322 - 0.483: 67 0.483 - 0.644: 3 0.644 - 0.806: 3 Chirality restraints: 3215 Sorted by residual: chirality pdb=" P G 2 25 " pdb=" OP1 G 2 25 " pdb=" OP2 G 2 25 " pdb=" O5' G 2 25 " both_signs ideal model delta sigma weight residual True 2.17 -2.98 -0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" P U 2 47 " pdb=" OP1 U 2 47 " pdb=" OP2 U 2 47 " pdb=" O5' U 2 47 " both_signs ideal model delta sigma weight residual True 2.17 -2.98 -0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA TYR 9 479 " pdb=" N TYR 9 479 " pdb=" C TYR 9 479 " pdb=" CB TYR 9 479 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 ... (remaining 3212 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 479 " -0.144 2.00e-02 2.50e+03 7.64e-02 1.17e+02 pdb=" CG TYR 9 479 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 479 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 479 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 479 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 479 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR 9 479 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR 9 479 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1165 " -0.125 2.00e-02 2.50e+03 7.25e-02 1.05e+02 pdb=" CG TYR A1165 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A1165 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A1165 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR A1165 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A1165 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A1165 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1165 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 357 " -0.106 2.00e-02 2.50e+03 5.68e-02 6.46e+01 pdb=" CG TYR C 357 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 357 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR C 357 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR C 357 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 357 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 357 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR C 357 " -0.083 2.00e-02 2.50e+03 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 15 2.48 - 3.09: 13488 3.09 - 3.69: 32747 3.69 - 4.30: 50015 4.30 - 4.90: 79944 Nonbonded interactions: 176209 Sorted by model distance: nonbonded pdb=" NH2 ARG C 728 " pdb=" OE1 GLU C1180 " model vdw 1.876 3.120 nonbonded pdb=" O GLY C 454 " pdb=" ND2 ASN C 760 " model vdw 2.275 3.120 nonbonded pdb=" NZ LYS C 126 " pdb=" OD1 ASP C 174 " model vdw 2.280 3.120 nonbonded pdb=" O ASN C 145 " pdb=" OG1 THR C 153 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASN C 550 " pdb=" N GLN C 551 " model vdw 2.326 3.120 ... (remaining 176204 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.012 0.804 20794 Z= 0.598 Angle : 1.524 24.197 28332 Z= 0.990 Chirality : 0.123 0.806 3215 Planarity : 0.010 0.159 3495 Dihedral : 15.439 92.927 7910 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 6.69 % Favored : 90.81 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 2399 helix: -1.36 (0.15), residues: 877 sheet: 0.35 (0.23), residues: 474 loop : -0.74 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.114 0.003 ARG C1013 TYR 0.144 0.013 TYR 9 479 PHE 0.052 0.008 PHE C 16 TRP 0.065 0.011 TRP p 170 HIS 0.026 0.005 HIS A1225 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.55 (20778) covalent geometry : angle 1.49991 / 0.99 (28312) hydrogen bonds : bond 0.16453 / 10.30 ( 976) hydrogen bonds : angle 7.72711 / 5.39 ( 2715) metal coordination : bond 0.29054 / 14.80 ( 16) metal coordination : angle 10.27254 / 5.21 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.814 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: B 461 THR cc_start: 0.8381 (t) cc_final: 0.7194 (p) REVERT: B 570 LYS cc_start: 0.7296 (tmtm) cc_final: 0.7095 (pmtt) REVERT: B 573 ASP cc_start: 0.7818 (m-30) cc_final: 0.7597 (m-30) REVERT: B 577 LYS cc_start: 0.6780 (tppt) cc_final: 0.6438 (mptt) REVERT: C 199 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 590 MET cc_start: 0.6931 (mtm) cc_final: 0.6432 (ptp) REVERT: C 702 PHE cc_start: 0.5379 (m-80) cc_final: 0.5086 (m-80) REVERT: 9 446 PHE cc_start: 0.8224 (m-80) cc_final: 0.7927 (m-80) REVERT: q 141 PRO cc_start: 0.6322 (Cg_exo) cc_final: 0.5418 (Cg_endo) REVERT: q 188 TYR cc_start: 0.8293 (m-80) cc_final: 0.8029 (m-80) REVERT: q 194 VAL cc_start: 0.8843 (t) cc_final: 0.8599 (m) REVERT: q 210 LYS cc_start: 0.6937 (tmtt) cc_final: 0.6328 (tmtt) REVERT: q 250 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6751 (ttp80) REVERT: A 517 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7931 (tpt90) REVERT: A 587 TYR cc_start: 0.8352 (t80) cc_final: 0.8117 (t80) REVERT: A 761 TYR cc_start: 0.8921 (m-80) cc_final: 0.8583 (m-80) REVERT: A 830 TYR cc_start: 0.7998 (t80) cc_final: 0.7623 (t80) REVERT: A 867 MET cc_start: 0.7983 (ttt) cc_final: 0.7474 (ttm) REVERT: A 876 MET cc_start: 0.7725 (mtp) cc_final: 0.7453 (mmm) REVERT: A 933 CYS cc_start: 0.7539 (t) cc_final: 0.6556 (t) REVERT: A 970 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7018 (pt) REVERT: A 978 LEU cc_start: 0.8440 (mt) cc_final: 0.8206 (mt) outliers start: 53 outliers final: 5 residues processed: 376 average time/residue: 0.7832 time to fit residues: 326.7585 Evaluate side-chains 211 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1147 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 458 ASN B 467 GLN C 219 HIS C 417 ASN C 791 HIS C 941 HIS C 983 ASN C 988 ASN ** C1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS E 35 GLN ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 488 ASN A 550 HIS A 829 ASN A 886 HIS A 903 GLN A1277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.152178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086157 restraints weight = 38787.962| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.75 r_work: 0.2910 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20794 Z= 0.183 Angle : 0.719 9.505 28332 Z= 0.372 Chirality : 0.048 0.288 3215 Planarity : 0.004 0.045 3495 Dihedral : 8.261 60.534 3158 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.17 % Allowed : 12.45 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2399 helix: 0.61 (0.17), residues: 901 sheet: 0.52 (0.23), residues: 504 loop : -0.05 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1027 TYR 0.025 0.002 TYR 9 479 PHE 0.033 0.002 PHE A 526 TRP 0.040 0.002 TRP p 170 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (20778) covalent geometry : angle 0.71176 / 0.37 (28312) hydrogen bonds : bond 0.04883 / 3.08 ( 976) hydrogen bonds : angle 5.49273 / 3.82 ( 2715) metal coordination : bond 0.01215 / 0.58 ( 16) metal coordination : angle 3.80807 / 2.01 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 THR cc_start: 0.8771 (t) cc_final: 0.8541 (p) REVERT: B 477 MET cc_start: 0.8668 (mmm) cc_final: 0.8319 (pmt) REVERT: B 478 HIS cc_start: 0.7713 (m170) cc_final: 0.7208 (m90) REVERT: C 146 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7908 (ttp80) REVERT: C 191 GLU cc_start: 0.8566 (mp0) cc_final: 0.8065 (pm20) REVERT: C 583 MET cc_start: 0.3420 (mpm) cc_final: 0.2349 (mpp) REVERT: C 590 MET cc_start: 0.7300 (mtm) cc_final: 0.6817 (ptp) REVERT: C 819 MET cc_start: 0.8611 (ttm) cc_final: 0.8381 (mtp) REVERT: E 48 ASP cc_start: 0.8299 (p0) cc_final: 0.8063 (p0) REVERT: q 194 VAL cc_start: 0.8800 (t) cc_final: 0.8582 (m) REVERT: q 210 LYS cc_start: 0.7627 (tmtt) cc_final: 0.7407 (tmtt) REVERT: q 242 MET cc_start: 0.7525 (mpp) cc_final: 0.6693 (mtp) REVERT: q 246 GLN cc_start: 0.8872 (mt0) cc_final: 0.8506 (mt0) REVERT: A 546 ASP cc_start: 0.7966 (m-30) cc_final: 0.7261 (t0) REVERT: A 587 TYR cc_start: 0.8345 (t80) cc_final: 0.8135 (t80) REVERT: A 675 MET cc_start: 0.8430 (mmm) cc_final: 0.8229 (mmm) REVERT: A 714 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: A 873 GLU cc_start: 0.8768 (pt0) cc_final: 0.8362 (pp20) REVERT: A 876 MET cc_start: 0.8134 (mtp) cc_final: 0.7830 (mmm) REVERT: A 971 MET cc_start: 0.8344 (mmm) cc_final: 0.7766 (mpt) REVERT: A 1167 TYR cc_start: 0.9011 (m-80) cc_final: 0.8809 (m-80) REVERT: p 157 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6148 (tm-30) outliers start: 46 outliers final: 13 residues processed: 257 average time/residue: 0.6501 time to fit residues: 187.9036 Evaluate side-chains 207 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain q residue 135 VAL Chi-restraints excluded: chain q residue 160 MET Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain p residue 157 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 193 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 GLN C 138 GLN C 206 GLN C 219 HIS C 818 GLN C 985 HIS C1147 HIS ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN A 886 HIS A 903 GLN A1002 ASN A1277 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.150002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081945 restraints weight = 37056.372| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.29 r_work: 0.2870 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20794 Z= 0.218 Angle : 0.686 14.116 28332 Z= 0.350 Chirality : 0.047 0.272 3215 Planarity : 0.004 0.040 3495 Dihedral : 7.522 60.319 3143 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.40 % Allowed : 13.39 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2399 helix: 0.96 (0.17), residues: 909 sheet: 0.41 (0.22), residues: 511 loop : 0.07 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 718 TYR 0.039 0.002 TYR 9 479 PHE 0.022 0.002 PHE C 702 TRP 0.035 0.002 TRP p 170 HIS 0.008 0.001 HIS C1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (20778) covalent geometry : angle 0.67737 / 0.35 (28312) hydrogen bonds : bond 0.04618 / 2.94 ( 976) hydrogen bonds : angle 5.20412 / 3.64 ( 2715) metal coordination : bond 0.00827 / 0.46 ( 16) metal coordination : angle 4.21411 / 2.20 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 THR cc_start: 0.8615 (t) cc_final: 0.8402 (p) REVERT: B 467 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8328 (tp40) REVERT: B 476 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: B 479 ASP cc_start: 0.8395 (m-30) cc_final: 0.8167 (m-30) REVERT: B 509 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8941 (mptp) REVERT: C 590 MET cc_start: 0.7202 (mtm) cc_final: 0.6767 (ptp) REVERT: C 818 GLN cc_start: 0.7903 (mt0) cc_final: 0.7450 (mp10) REVERT: C 819 MET cc_start: 0.8546 (ttm) cc_final: 0.8325 (mtp) REVERT: G 27 ASP cc_start: 0.9307 (t0) cc_final: 0.9061 (t70) REVERT: q 194 VAL cc_start: 0.8902 (t) cc_final: 0.8681 (m) REVERT: q 195 GLU cc_start: 0.8316 (mp0) cc_final: 0.7847 (mp0) REVERT: q 242 MET cc_start: 0.7669 (mpp) cc_final: 0.6777 (mtp) REVERT: q 246 GLN cc_start: 0.8936 (mt0) cc_final: 0.8547 (mt0) REVERT: q 250 ARG cc_start: 0.8445 (ptt90) cc_final: 0.8153 (ptt90) REVERT: A 501 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8617 (pp) REVERT: A 546 ASP cc_start: 0.7993 (m-30) cc_final: 0.7227 (t0) REVERT: A 675 MET cc_start: 0.8326 (mmm) cc_final: 0.8079 (mmm) REVERT: A 714 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: A 830 TYR cc_start: 0.8679 (t80) cc_final: 0.8274 (t80) REVERT: A 873 GLU cc_start: 0.8790 (pt0) cc_final: 0.8420 (pt0) REVERT: A 903 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: p 157 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.6147 (tm-30) outliers start: 51 outliers final: 14 residues processed: 244 average time/residue: 0.6046 time to fit residues: 168.5076 Evaluate side-chains 215 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain q residue 160 MET Chi-restraints excluded: chain q residue 186 CYS Chi-restraints excluded: chain q residue 215 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 903 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1260 LYS Chi-restraints excluded: chain p residue 157 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 88 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 93 optimal weight: 0.0770 chunk 199 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 HIS ** A 950 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 = 0.4242 r_free = 0.4242 target = 0.150993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085363 restraints weight = 42556.033| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.07 r_work: 0.2862 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20794 Z= 0.156 Angle : 0.640 13.470 28332 Z= 0.322 Chirality : 0.045 0.267 3215 Planarity : 0.004 0.040 3495 Dihedral : 7.336 61.175 3142 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.03 % Allowed : 14.10 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2399 helix: 1.12 (0.17), residues: 915 sheet: 0.51 (0.23), residues: 492 loop : -0.01 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG q 250 TYR 0.022 0.001 TYR A 587 PHE 0.015 0.001 PHE A1155 TRP 0.032 0.002 TRP p 170 HIS 0.015 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (20778) covalent geometry : angle 0.63371 / 0.32 (28312) hydrogen bonds : bond 0.04060 / 2.59 ( 976) hydrogen bonds : angle 5.06436 / 3.54 ( 2715) metal coordination : bond 0.00546 / 0.31 ( 16) metal coordination : angle 3.52292 / 1.84 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8532 (tp40) REVERT: B 509 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8906 (mptp) REVERT: C 460 TRP cc_start: 0.6214 (m-90) cc_final: 0.5679 (m-90) REVERT: C 583 MET cc_start: 0.3397 (mpm) cc_final: 0.2157 (mpp) REVERT: C 590 MET cc_start: 0.7028 (mtm) cc_final: 0.6583 (ptp) REVERT: C 645 MET cc_start: 0.7748 (ptm) cc_final: 0.7465 (pmm) REVERT: C 818 GLN cc_start: 0.7897 (mt0) cc_final: 0.7447 (mp10) REVERT: C 819 MET cc_start: 0.8516 (ttm) cc_final: 0.8257 (mtp) REVERT: C 1090 GLU cc_start: 0.8877 (pt0) cc_final: 0.8577 (pt0) REVERT: C 1146 MET cc_start: 0.9104 (mtp) cc_final: 0.8870 (ttp) REVERT: G 27 ASP cc_start: 0.9283 (t0) cc_final: 0.9028 (t70) REVERT: q 194 VAL cc_start: 0.8895 (t) cc_final: 0.8671 (m) REVERT: q 195 GLU cc_start: 0.8279 (mp0) cc_final: 0.7801 (mp0) REVERT: q 242 MET cc_start: 0.7679 (mpp) cc_final: 0.6802 (mtp) REVERT: q 246 GLN cc_start: 0.8916 (mt0) cc_final: 0.8514 (mt0) REVERT: A 501 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 546 ASP cc_start: 0.8048 (m-30) cc_final: 0.7220 (t0) REVERT: A 626 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.7107 (m-40) REVERT: A 830 TYR cc_start: 0.8576 (t80) cc_final: 0.8205 (t80) REVERT: A 873 GLU cc_start: 0.8770 (pt0) cc_final: 0.8418 (pt0) REVERT: A 971 MET cc_start: 0.8403 (mmm) cc_final: 0.7839 (mpt) outliers start: 43 outliers final: 12 residues processed: 231 average time/residue: 0.5990 time to fit residues: 157.8098 Evaluate side-chains 205 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain q residue 160 MET Chi-restraints excluded: chain q residue 186 CYS Chi-restraints excluded: chain q residue 209 TYR Chi-restraints excluded: chain q residue 240 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1260 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 221 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 224 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN A 886 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.149995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084734 restraints weight = 44715.433| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.85 r_work: 0.2862 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20794 Z= 0.177 Angle : 0.646 12.145 28332 Z= 0.324 Chirality : 0.045 0.264 3215 Planarity : 0.004 0.041 3495 Dihedral : 7.193 61.184 3140 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.84 % Allowed : 14.57 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2399 helix: 1.21 (0.18), residues: 912 sheet: 0.46 (0.23), residues: 499 loop : 0.00 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 517 TYR 0.027 0.002 TYR A 898 PHE 0.027 0.002 PHE C 261 TRP 0.029 0.002 TRP p 170 HIS 0.009 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (20778) covalent geometry : angle 0.63960 / 0.32 (28312) hydrogen bonds : bond 0.04081 / 2.60 ( 976) hydrogen bonds : angle 5.01228 / 3.51 ( 2715) metal coordination : bond 0.00571 / 0.33 ( 16) metal coordination : angle 3.59139 / 1.86 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8635 (tp40) REVERT: C 460 TRP cc_start: 0.6217 (OUTLIER) cc_final: 0.5650 (m-90) REVERT: C 583 MET cc_start: 0.3388 (mpm) cc_final: 0.2174 (mpp) REVERT: C 590 MET cc_start: 0.7030 (mtm) cc_final: 0.6666 (ptp) REVERT: C 645 MET cc_start: 0.7689 (ptm) cc_final: 0.7425 (pmm) REVERT: C 706 MET cc_start: 0.8048 (mmm) cc_final: 0.7724 (pmt) REVERT: C 718 ARG cc_start: 0.5938 (mtp85) cc_final: 0.5613 (mtp85) REVERT: C 818 GLN cc_start: 0.7914 (mt0) cc_final: 0.7463 (mp10) REVERT: C 819 MET cc_start: 0.8520 (ttm) cc_final: 0.8264 (mtp) REVERT: C 936 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8933 (tttp) REVERT: C 1090 GLU cc_start: 0.8875 (pt0) cc_final: 0.8535 (pt0) REVERT: C 1146 MET cc_start: 0.9107 (mtp) cc_final: 0.8890 (ttp) REVERT: G 27 ASP cc_start: 0.9299 (t0) cc_final: 0.9056 (t70) REVERT: q 194 VAL cc_start: 0.8919 (t) cc_final: 0.8682 (m) REVERT: q 195 GLU cc_start: 0.8298 (mp0) cc_final: 0.7816 (mp0) REVERT: q 242 MET cc_start: 0.7716 (mpp) cc_final: 0.7513 (mpm) REVERT: q 246 GLN cc_start: 0.8922 (mt0) cc_final: 0.8527 (mt0) REVERT: A 501 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8562 (pp) REVERT: A 546 ASP cc_start: 0.8041 (m-30) cc_final: 0.7253 (t0) REVERT: A 626 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.7155 (m-40) REVERT: A 675 MET cc_start: 0.8251 (mmm) cc_final: 0.8022 (mmm) REVERT: A 714 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: A 830 TYR cc_start: 0.8572 (t80) cc_final: 0.8222 (t80) REVERT: A 873 GLU cc_start: 0.8763 (pt0) cc_final: 0.8431 (pt0) REVERT: A 898 TYR cc_start: 0.7736 (t80) cc_final: 0.7107 (t80) REVERT: A 971 MET cc_start: 0.8300 (mmm) cc_final: 0.7773 (mpt) outliers start: 39 outliers final: 15 residues processed: 224 average time/residue: 0.6090 time to fit residues: 155.6977 Evaluate side-chains 209 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain q residue 160 MET Chi-restraints excluded: chain q residue 186 CYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1260 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 208 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086438 restraints weight = 43514.335| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.10 r_work: 0.2858 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20794 Z= 0.147 Angle : 0.626 11.032 28332 Z= 0.313 Chirality : 0.044 0.261 3215 Planarity : 0.004 0.042 3495 Dihedral : 7.079 61.290 3140 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.70 % Allowed : 15.04 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2399 helix: 1.28 (0.18), residues: 916 sheet: 0.48 (0.23), residues: 498 loop : 0.05 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 517 TYR 0.021 0.001 TYR A 898 PHE 0.026 0.001 PHE 9 422 TRP 0.027 0.002 TRP p 170 HIS 0.027 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (20778) covalent geometry : angle 0.62015 / 0.31 (28312) hydrogen bonds : bond 0.03900 / 2.49 ( 976) hydrogen bonds : angle 4.92120 / 3.44 ( 2715) metal coordination : bond 0.00461 / 0.26 ( 16) metal coordination : angle 3.40019 / 1.74 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8672 (tp40) REVERT: C 460 TRP cc_start: 0.6157 (OUTLIER) cc_final: 0.5601 (m-90) REVERT: C 583 MET cc_start: 0.3391 (mpm) cc_final: 0.2189 (mpp) REVERT: C 590 MET cc_start: 0.6912 (mtm) cc_final: 0.6560 (ptp) REVERT: C 645 MET cc_start: 0.7698 (ptm) cc_final: 0.7425 (pmm) REVERT: C 818 GLN cc_start: 0.7916 (mt0) cc_final: 0.7468 (mp10) REVERT: C 819 MET cc_start: 0.8473 (ttm) cc_final: 0.8221 (mtp) REVERT: C 1090 GLU cc_start: 0.8917 (pt0) cc_final: 0.8610 (pt0) REVERT: G 27 ASP cc_start: 0.9282 (t0) cc_final: 0.9051 (t70) REVERT: q 194 VAL cc_start: 0.8912 (t) cc_final: 0.8656 (m) REVERT: q 195 GLU cc_start: 0.8285 (mp0) cc_final: 0.7657 (mp0) REVERT: q 246 GLN cc_start: 0.8899 (mt0) cc_final: 0.8516 (mt0) REVERT: A 501 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8513 (pp) REVERT: A 546 ASP cc_start: 0.8075 (m-30) cc_final: 0.7336 (t0) REVERT: A 626 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.7161 (m-40) REVERT: A 675 MET cc_start: 0.8251 (mmm) cc_final: 0.8037 (mmm) REVERT: A 830 TYR cc_start: 0.8519 (t80) cc_final: 0.8154 (t80) REVERT: A 971 MET cc_start: 0.8379 (mmm) cc_final: 0.8086 (mpp) outliers start: 36 outliers final: 15 residues processed: 221 average time/residue: 0.6028 time to fit residues: 152.2790 Evaluate side-chains 206 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain q residue 160 MET Chi-restraints excluded: chain q residue 186 CYS Chi-restraints excluded: chain q residue 215 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1260 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 203 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 159 optimal weight: 0.0050 chunk 101 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 107 optimal weight: 0.0010 chunk 109 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 57 optimal weight: 0.0170 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN A 886 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.150647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083378 restraints weight = 37249.533| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.31 r_work: 0.2909 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20794 Z= 0.135 Angle : 0.616 11.006 28332 Z= 0.305 Chirality : 0.044 0.255 3215 Planarity : 0.004 0.040 3495 Dihedral : 6.952 61.263 3140 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.56 % Allowed : 15.37 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2399 helix: 1.41 (0.18), residues: 912 sheet: 0.52 (0.23), residues: 498 loop : 0.12 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG q 250 TYR 0.026 0.001 TYR A 898 PHE 0.013 0.001 PHE A1153 TRP 0.026 0.002 TRP p 170 HIS 0.008 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20778) covalent geometry : angle 0.60989 / 0.30 (28312) hydrogen bonds : bond 0.03713 / 2.37 ( 976) hydrogen bonds : angle 4.83317 / 3.39 ( 2715) metal coordination : bond 0.00442 / 0.26 ( 16) metal coordination : angle 3.34972 / 1.73 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 457 MET cc_start: 0.8115 (tmm) cc_final: 0.7376 (mtt) REVERT: B 477 MET cc_start: 0.8878 (mmm) cc_final: 0.8350 (pmt) REVERT: C 460 TRP cc_start: 0.6101 (OUTLIER) cc_final: 0.5517 (m-90) REVERT: C 583 MET cc_start: 0.3263 (mpm) cc_final: 0.2048 (mpp) REVERT: C 590 MET cc_start: 0.6953 (mtm) cc_final: 0.6563 (ptp) REVERT: C 645 MET cc_start: 0.7590 (ptm) cc_final: 0.7337 (pmm) REVERT: C 818 GLN cc_start: 0.7926 (mt0) cc_final: 0.7499 (mp10) REVERT: C 819 MET cc_start: 0.8470 (ttm) cc_final: 0.8221 (mtp) REVERT: C 1090 GLU cc_start: 0.8886 (pt0) cc_final: 0.8601 (pt0) REVERT: G 27 ASP cc_start: 0.9217 (t0) cc_final: 0.8996 (t70) REVERT: q 194 VAL cc_start: 0.8924 (t) cc_final: 0.8666 (m) REVERT: q 195 GLU cc_start: 0.8299 (mp0) cc_final: 0.7675 (mp0) REVERT: q 242 MET cc_start: 0.7990 (mpm) cc_final: 0.7116 (mtp) REVERT: q 246 GLN cc_start: 0.8902 (mt0) cc_final: 0.8517 (mt0) REVERT: A 501 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8495 (pp) REVERT: A 546 ASP cc_start: 0.8098 (m-30) cc_final: 0.7381 (t0) REVERT: A 602 LYS cc_start: 0.7897 (tmmt) cc_final: 0.7677 (pptt) REVERT: A 626 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.7185 (m-40) REVERT: A 804 ASN cc_start: 0.9373 (t0) cc_final: 0.9145 (p0) REVERT: A 971 MET cc_start: 0.8333 (mmm) cc_final: 0.8008 (mmm) REVERT: A 981 TYR cc_start: 0.7786 (m-80) cc_final: 0.7499 (m-80) outliers start: 33 outliers final: 10 residues processed: 219 average time/residue: 0.5938 time to fit residues: 148.2030 Evaluate side-chains 204 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 139 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 196 optimal weight: 0.0670 chunk 220 optimal weight: 0.1980 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 GLN C 219 HIS ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN q 212 HIS A 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.150875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083758 restraints weight = 37284.158| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.30 r_work: 0.2920 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20794 Z= 0.125 Angle : 0.620 10.849 28332 Z= 0.305 Chirality : 0.044 0.249 3215 Planarity : 0.004 0.044 3495 Dihedral : 6.883 61.325 3140 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.27 % Allowed : 15.94 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2399 helix: 1.43 (0.18), residues: 916 sheet: 0.57 (0.23), residues: 498 loop : 0.14 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG q 250 TYR 0.031 0.001 TYR A 898 PHE 0.019 0.001 PHE 9 422 TRP 0.024 0.002 TRP p 170 HIS 0.007 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (20778) covalent geometry : angle 0.61374 / 0.30 (28312) hydrogen bonds : bond 0.03626 / 2.31 ( 976) hydrogen bonds : angle 4.78548 / 3.36 ( 2715) metal coordination : bond 0.00413 / 0.23 ( 16) metal coordination : angle 3.38494 / 1.76 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 MET cc_start: 0.8110 (tmm) cc_final: 0.7332 (mtm) REVERT: C 191 GLU cc_start: 0.8634 (mp0) cc_final: 0.8003 (pm20) REVERT: C 320 ASP cc_start: 0.8000 (t0) cc_final: 0.7666 (t70) REVERT: C 460 TRP cc_start: 0.6047 (OUTLIER) cc_final: 0.5446 (m-90) REVERT: C 583 MET cc_start: 0.3228 (mpm) cc_final: 0.2027 (mpp) REVERT: C 590 MET cc_start: 0.6937 (mtm) cc_final: 0.6546 (ptp) REVERT: C 645 MET cc_start: 0.7511 (ptm) cc_final: 0.7254 (pmm) REVERT: C 663 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8356 (pp) REVERT: C 818 GLN cc_start: 0.7923 (mt0) cc_final: 0.7497 (mp10) REVERT: C 819 MET cc_start: 0.8458 (ttm) cc_final: 0.8213 (mtp) REVERT: C 1090 GLU cc_start: 0.8877 (pt0) cc_final: 0.8611 (pt0) REVERT: C 1143 HIS cc_start: 0.8622 (t70) cc_final: 0.8200 (m-70) REVERT: G 27 ASP cc_start: 0.9184 (t0) cc_final: 0.8979 (t70) REVERT: q 194 VAL cc_start: 0.8943 (t) cc_final: 0.8672 (m) REVERT: q 195 GLU cc_start: 0.8267 (mp0) cc_final: 0.7664 (mp0) REVERT: q 242 MET cc_start: 0.8015 (mpm) cc_final: 0.7235 (mtp) REVERT: q 246 GLN cc_start: 0.8880 (mt0) cc_final: 0.8567 (mt0) REVERT: A 501 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8492 (pp) REVERT: A 516 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8024 (mt) REVERT: A 546 ASP cc_start: 0.8154 (m-30) cc_final: 0.7447 (t0) REVERT: A 595 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8658 (pt0) REVERT: A 614 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7957 (tmm160) REVERT: A 830 TYR cc_start: 0.8653 (t80) cc_final: 0.8106 (t80) REVERT: A 971 MET cc_start: 0.8302 (mmm) cc_final: 0.8076 (mmm) outliers start: 27 outliers final: 11 residues processed: 215 average time/residue: 0.5997 time to fit residues: 146.9454 Evaluate side-chains 204 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain 9 residue 425 HIS Chi-restraints excluded: chain q residue 160 MET Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 164 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 218 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 156 optimal weight: 0.0870 chunk 79 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 GLN B 503 HIS C 219 HIS 9 423 GLN ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 448 ASN q 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084623 restraints weight = 39492.774| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.07 r_work: 0.2841 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20794 Z= 0.177 Angle : 0.647 10.916 28332 Z= 0.319 Chirality : 0.045 0.245 3215 Planarity : 0.004 0.041 3495 Dihedral : 6.935 61.174 3140 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.46 % Allowed : 16.08 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2399 helix: 1.41 (0.18), residues: 915 sheet: 0.53 (0.23), residues: 502 loop : 0.11 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG q 250 TYR 0.026 0.002 TYR A 898 PHE 0.020 0.002 PHE A1153 TRP 0.023 0.002 TRP p 170 HIS 0.007 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (20778) covalent geometry : angle 0.63871 / 0.32 (28312) hydrogen bonds : bond 0.03980 / 2.55 ( 976) hydrogen bonds : angle 4.82969 / 3.39 ( 2715) metal coordination : bond 0.00578 / 0.33 ( 16) metal coordination : angle 3.98427 / 2.05 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 MET cc_start: 0.8174 (tmm) cc_final: 0.7401 (mtm) REVERT: B 477 MET cc_start: 0.8905 (mmm) cc_final: 0.8418 (pmt) REVERT: C 298 MET cc_start: 0.8164 (pp-130) cc_final: 0.7839 (pp-130) REVERT: C 460 TRP cc_start: 0.6068 (m-90) cc_final: 0.5538 (m-90) REVERT: C 590 MET cc_start: 0.6840 (mtm) cc_final: 0.6521 (ptp) REVERT: C 645 MET cc_start: 0.7551 (ptm) cc_final: 0.7293 (pmm) REVERT: C 818 GLN cc_start: 0.7919 (mt0) cc_final: 0.7489 (mp10) REVERT: C 819 MET cc_start: 0.8450 (ttm) cc_final: 0.8161 (mtp) REVERT: C 1090 GLU cc_start: 0.8925 (pt0) cc_final: 0.8644 (pt0) REVERT: C 1137 ASP cc_start: 0.9180 (m-30) cc_final: 0.8949 (m-30) REVERT: C 1143 HIS cc_start: 0.8664 (t70) cc_final: 0.8284 (m-70) REVERT: q 194 VAL cc_start: 0.8908 (t) cc_final: 0.8650 (m) REVERT: q 195 GLU cc_start: 0.8270 (mp0) cc_final: 0.7643 (mp0) REVERT: q 242 MET cc_start: 0.8045 (mpm) cc_final: 0.7293 (mtp) REVERT: q 246 GLN cc_start: 0.8903 (mt0) cc_final: 0.8568 (mt0) REVERT: A 501 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8486 (pp) REVERT: A 546 ASP cc_start: 0.8175 (m-30) cc_final: 0.7454 (t0) REVERT: A 614 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7998 (tmm160) REVERT: A 830 TYR cc_start: 0.8580 (t80) cc_final: 0.8168 (t80) REVERT: A 1228 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8441 (mp10) outliers start: 31 outliers final: 9 residues processed: 213 average time/residue: 0.5694 time to fit residues: 138.3296 Evaluate side-chains 196 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1217 PHE Chi-restraints excluded: chain 9 residue 425 HIS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1228 GLN Chi-restraints excluded: chain A residue 1291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 30 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 109 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS C 983 ASN ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.150036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082448 restraints weight = 38313.427| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.33 r_work: 0.2889 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20794 Z= 0.149 Angle : 0.645 12.603 28332 Z= 0.317 Chirality : 0.044 0.243 3215 Planarity : 0.004 0.044 3495 Dihedral : 6.914 61.468 3140 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.90 % Allowed : 16.83 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2399 helix: 1.42 (0.18), residues: 918 sheet: 0.55 (0.23), residues: 498 loop : 0.12 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG q 250 TYR 0.025 0.001 TYR A 898 PHE 0.019 0.001 PHE 9 422 TRP 0.023 0.002 TRP p 170 HIS 0.007 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (20778) covalent geometry : angle 0.63859 / 0.32 (28312) hydrogen bonds : bond 0.03783 / 2.43 ( 976) hydrogen bonds : angle 4.79674 / 3.37 ( 2715) metal coordination : bond 0.00501 / 0.27 ( 16) metal coordination : angle 3.39834 / 1.82 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 MET cc_start: 0.8168 (tmm) cc_final: 0.7485 (mtt) REVERT: B 477 MET cc_start: 0.8864 (mmm) cc_final: 0.8430 (pmt) REVERT: C 298 MET cc_start: 0.8186 (pp-130) cc_final: 0.7839 (pp-130) REVERT: C 460 TRP cc_start: 0.6048 (m-90) cc_final: 0.5442 (m-90) REVERT: C 568 MET cc_start: 0.3944 (tpt) cc_final: 0.3610 (tpt) REVERT: C 583 MET cc_start: 0.3305 (mpm) cc_final: 0.3076 (mpm) REVERT: C 590 MET cc_start: 0.6915 (mtm) cc_final: 0.6549 (ptp) REVERT: C 645 MET cc_start: 0.7485 (ptm) cc_final: 0.7195 (pmt) REVERT: C 818 GLN cc_start: 0.7910 (mt0) cc_final: 0.7483 (mp10) REVERT: C 819 MET cc_start: 0.8446 (ttm) cc_final: 0.8169 (mtp) REVERT: C 1090 GLU cc_start: 0.8884 (pt0) cc_final: 0.8616 (pt0) REVERT: C 1137 ASP cc_start: 0.9125 (m-30) cc_final: 0.8902 (m-30) REVERT: C 1143 HIS cc_start: 0.8627 (t70) cc_final: 0.8228 (m-70) REVERT: q 160 MET cc_start: 0.5627 (pmm) cc_final: 0.5076 (mpt) REVERT: q 194 VAL cc_start: 0.8944 (t) cc_final: 0.8682 (m) REVERT: q 195 GLU cc_start: 0.8250 (mp0) cc_final: 0.7627 (mp0) REVERT: q 242 MET cc_start: 0.8050 (mpm) cc_final: 0.7311 (mtp) REVERT: q 246 GLN cc_start: 0.8906 (mt0) cc_final: 0.8585 (mt0) REVERT: A 501 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8449 (pp) REVERT: A 546 ASP cc_start: 0.8188 (m-30) cc_final: 0.7491 (t0) REVERT: A 614 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8049 (tmm160) REVERT: A 830 TYR cc_start: 0.8635 (t80) cc_final: 0.8260 (t80) REVERT: A 1009 MET cc_start: 0.7640 (pp-130) cc_final: 0.7359 (tmm) REVERT: A 1228 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8392 (mp10) outliers start: 19 outliers final: 8 residues processed: 207 average time/residue: 0.6127 time to fit residues: 144.8318 Evaluate side-chains 197 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain 9 residue 425 HIS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1007 HIS Chi-restraints excluded: chain A residue 1228 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 189 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 223 optimal weight: 0.0770 chunk 74 optimal weight: 7.9990 chunk 179 optimal weight: 0.0170 chunk 160 optimal weight: 0.8980 chunk 216 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 215 optimal weight: 0.0870 chunk 198 optimal weight: 5.9990 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 9 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.151215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086629 restraints weight = 47433.033| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.01 r_work: 0.2914 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 20794 Z= 0.113 Angle : 0.624 12.100 28332 Z= 0.307 Chirality : 0.043 0.237 3215 Planarity : 0.004 0.041 3495 Dihedral : 6.797 61.581 3140 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.61 % Allowed : 17.16 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2399 helix: 1.47 (0.18), residues: 918 sheet: 0.58 (0.23), residues: 490 loop : 0.19 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG q 250 TYR 0.015 0.001 TYR A 830 PHE 0.015 0.001 PHE A 532 TRP 0.020 0.002 TRP p 170 HIS 0.008 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20778) covalent geometry : angle 0.62038 / 0.31 (28312) hydrogen bonds : bond 0.03478 / 2.22 ( 976) hydrogen bonds : angle 4.72295 / 3.32 ( 2715) metal coordination : bond 0.00359 / 0.19 ( 16) metal coordination : angle 2.56757 / 1.40 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15948.57 seconds wall clock time: 270 minutes 17.03 seconds (16217.03 seconds total)