Starting phenix.real_space_refine on Sun Aug 9 10:30:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sc3_54748/08_2026/9sc3_54748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sc3_54748/08_2026/9sc3_54748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sc3_54748/08_2026/9sc3_54748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sc3_54748/08_2026/9sc3_54748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sc3_54748/08_2026/9sc3_54748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sc3_54748/08_2026/9sc3_54748.map" } resolution = 3.68 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= 0.031 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 105.454 70.772 94.861 1.00183.41 S ATOM 479 SG CYS A 70 104.876 67.260 93.542 1.00188.18 S ATOM 532 SG CYS A 77 102.221 70.009 93.060 1.00170.27 S ATOM 762 SG CYS A 107 80.315 76.946 135.137 1.00212.48 S ATOM 786 SG CYS A 110 81.712 73.608 135.804 1.00206.11 S ATOM 1091 SG CYS A 148 78.282 74.473 137.265 1.00218.92 S ATOM 1105 SG CYS A 167 81.469 76.055 138.669 1.00220.44 S ATOM 19603 SG CYS B1163 97.445 58.596 105.081 1.00181.90 S ATOM 19621 SG CYS B1166 95.859 61.893 105.433 1.00190.39 S ATOM 19746 SG CYS B1182 99.689 61.582 104.781 1.00190.96 S ATOM 19765 SG CYS B1185 98.116 60.794 108.204 1.00189.33 S ATOM 20753 SG CYS C 86 91.622 74.997 25.713 1.00216.05 S ATOM 20770 SG CYS C 88 93.868 77.138 27.766 1.00223.87 S ATOM 20803 SG CYS C 92 92.999 78.251 24.384 1.00203.06 S ATOM 20826 SG CYS C 95 90.278 78.325 27.117 1.00198.40 S ATOM 28411 SG CYS I 7 40.563 125.144 128.397 1.00279.56 S ATOM 28436 SG CYS I 10 44.182 124.097 127.937 1.00276.74 S ATOM 28602 SG CYS I 29 41.809 121.934 130.060 1.00284.43 S ATOM 28626 SG CYS I 32 42.924 125.240 131.356 1.00286.48 S ATOM 28953 SG CYS I 75 15.798 115.782 90.386 1.00278.30 S ATOM 28975 SG CYS I 78 15.497 119.305 89.129 1.00277.57 S ATOM 29191 SG CYS I 103 18.868 117.593 88.983 1.00268.40 S ATOM 29211 SG CYS I 106 17.413 118.669 92.328 1.00271.40 S ATOM 29313 SG CYS J 7 62.770 90.452 37.689 1.00162.33 S ATOM 29336 SG CYS J 10 62.424 88.278 34.547 1.00151.26 S ATOM 29616 SG CYS J 45 59.348 89.241 36.656 1.00164.35 S ATOM 29622 SG CYS J 46 61.185 91.646 34.344 1.00168.40 S ATOM 30745 SG CYS L 31 95.916 114.027 53.843 1.00250.73 S ATOM 30765 SG CYS L 34 97.230 115.727 50.641 1.00249.69 S ATOM 30869 SG CYS L 48 99.493 114.680 53.525 1.00254.15 S ATOM 30892 SG CYS L 51 97.184 117.694 53.862 1.00262.36 S Time building chain proxies: 6.56, per 1000 atoms: 0.20 Number of scatterers: 33083 At special positions: 0 Unit cell: (151.241, 154.505, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 70 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 48 sheets defined 38.8% alpha, 20.1% beta 41 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.679A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.855A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.573A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.615A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.511A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.682A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.947A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.554A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.958A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.503A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.589A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1087 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.663A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.805A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.794A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.959A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.970A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 4.523A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.617A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.663A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.814A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.612A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 751 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.857A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.701A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.530A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.283A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.889A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.574A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.501A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.509A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.196A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.539A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.598A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 5 through 27 removed outlier: 3.572A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.554A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 55 through 59 removed outlier: 4.125A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.909A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.647A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.604A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.803A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.892A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 42 through 52 removed outlier: 3.510A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 3.563A pdb=" N VAL A 241 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.729A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.643A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.821A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.511A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 587 through 590 removed outlier: 7.178A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.629A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.290A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.686A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.686A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.841A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.841A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.165A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.712A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 641 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.256A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.601A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.601A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.322A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.593A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.964A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.704A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.592A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.916A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.486A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.799A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.408A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.868A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.567A pdb=" N ARG I 17 " --> pdb=" O LEU I 26 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.071A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 1373 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 9.77 Time building geometry restraints manager: 3.77 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: 5405 1.31 - 1.43: 8967 1.43 - 1.56: 19013 1.56 - 1.69: 196 1.69 - 1.81: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP R 101 " pdb=" N9 ATP R 101 " ideal model delta sigma weight residual 1.374 1.181 0.193 1.00e-02 1.00e+04 3.74e+02 bond pdb=" C8 ATP R 101 " pdb=" N9 ATP R 101 " ideal model delta sigma weight residual 1.370 1.209 0.161 1.20e-02 6.94e+03 1.81e+02 bond pdb=" C6 ATP R 101 " pdb=" N6 ATP R 101 " ideal model delta sigma weight residual 1.337 1.447 -0.110 1.10e-02 8.26e+03 1.00e+02 bond pdb=" C5 ATP R 101 " pdb=" C6 ATP R 101 " ideal model delta sigma weight residual 1.409 1.333 0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C5 ATP R 101 " pdb=" N7 ATP R 101 " ideal model delta sigma weight residual 1.387 1.451 -0.064 1.00e-02 1.00e+04 4.11e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 46022 3.96 - 7.91: 126 7.91 - 11.87: 2 11.87 - 15.83: 2 15.83 - 19.78: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP R 101 " pdb=" O3B ATP R 101 " pdb=" PG ATP R 101 " ideal model delta sigma weight residual 139.87 120.09 19.78 1.00e+00 1.00e+00 3.91e+02 angle pdb=" PA ATP R 101 " pdb=" O3A ATP R 101 " pdb=" PB ATP R 101 " ideal model delta sigma weight residual 136.83 122.07 14.76 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C4 ATP R 101 " pdb=" N9 ATP R 101 " pdb=" C8 ATP R 101 " ideal model delta sigma weight residual 105.72 119.56 -13.84 1.00e+00 1.00e+00 1.91e+02 angle pdb=" N1 ATP R 101 " pdb=" C2 ATP R 101 " pdb=" N3 ATP R 101 " ideal model delta sigma weight residual 128.69 120.22 8.47 1.00e+00 1.00e+00 7.18e+01 angle pdb=" C GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 19797 31.50 - 63.01: 622 63.01 - 94.51: 44 94.51 - 126.01: 1 126.01 - 157.51: 3 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DC N 38 " pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " pdb=" P DC N 39 " ideal model delta sinusoidal sigma weight residual -140.00 17.51 -157.51 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3412 0.033 - 0.066: 1153 0.066 - 0.099: 374 0.099 - 0.132: 230 0.132 - 0.165: 21 Chirality restraints: 5190 Sorted by residual: chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" C3' DG N 58 " pdb=" C4' DG N 58 " pdb=" O3' DG N 58 " pdb=" C2' DG N 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.89 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C LEU A 710 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A1099 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.033 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 245 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.028 5.00e-02 4.00e+02 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 90 2.38 - 3.01: 18842 3.01 - 3.64: 49523 3.64 - 4.27: 75321 4.27 - 4.90: 125930 Nonbonded interactions: 269706 Sorted by model distance: nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1801 " model vdw 1.753 2.170 nonbonded pdb="MG MG A1801 " pdb=" O2A ATP R 101 " model vdw 1.802 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1801 " model vdw 1.884 2.170 nonbonded pdb="MG MG A1801 " pdb=" O2G ATP R 101 " model vdw 1.891 2.170 nonbonded pdb="MG MG A1802 " pdb=" O2A ATP R 101 " model vdw 1.954 2.170 ... (remaining 269701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.004 0.193 33905 Z= 0.315 Angle : 0.619 19.782 46198 Z= 0.415 Chirality : 0.042 0.165 5190 Planarity : 0.004 0.050 5630 Dihedral : 14.530 157.515 13127 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.69 (0.14), residues: 3854 helix: 1.83 (0.15), residues: 1296 sheet: 0.16 (0.22), residues: 607 loop : -0.35 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 320 TYR 0.022 0.001 TYR B1092 PHE 0.019 0.001 PHE B 37 TRP 0.011 0.001 TRP B 561 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.32 (33873) covalent geometry : angle 0.61364 / 0.41 (46153) hydrogen bonds : bond 0.19225 / 12.76 ( 1436) hydrogen bonds : angle 6.78373 / 4.92 ( 3985) metal coordination : bond 0.00655 / 0.43 ( 32) metal coordination : angle 2.70770 / 1.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 774 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8901 (mp0) cc_final: 0.8671 (pm20) REVERT: A 122 MET cc_start: 0.8973 (tpp) cc_final: 0.8676 (tpp) REVERT: A 218 ASP cc_start: 0.9126 (m-30) cc_final: 0.8763 (m-30) REVERT: A 277 GLU cc_start: 0.9550 (tt0) cc_final: 0.8963 (tm-30) REVERT: A 453 MET cc_start: 0.8970 (mpp) cc_final: 0.8456 (mtm) REVERT: A 456 MET cc_start: 0.9330 (mtm) cc_final: 0.8941 (mtp) REVERT: A 487 MET cc_start: 0.9497 (mtp) cc_final: 0.9033 (mtp) REVERT: A 605 MET cc_start: 0.9215 (tpt) cc_final: 0.8551 (tpp) REVERT: A 698 GLN cc_start: 0.8601 (tt0) cc_final: 0.8308 (tt0) REVERT: A 795 GLU cc_start: 0.8974 (pm20) cc_final: 0.8754 (pm20) REVERT: A 847 ASP cc_start: 0.8710 (p0) cc_final: 0.8027 (p0) REVERT: A 873 MET cc_start: 0.8889 (mmp) cc_final: 0.8032 (mmp) REVERT: A 919 ILE cc_start: 0.8724 (mm) cc_final: 0.8486 (pt) REVERT: A 992 ASP cc_start: 0.9048 (m-30) cc_final: 0.8586 (t70) REVERT: A 1003 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8548 (mmmt) REVERT: A 1206 ASP cc_start: 0.9436 (t0) cc_final: 0.9180 (m-30) REVERT: A 1237 ILE cc_start: 0.8923 (pt) cc_final: 0.8476 (mm) REVERT: A 1276 VAL cc_start: 0.7739 (t) cc_final: 0.7531 (t) REVERT: A 1307 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8443 (mt-10) REVERT: A 1450 LEU cc_start: 0.9349 (tp) cc_final: 0.9108 (tt) REVERT: B 74 LEU cc_start: 0.8590 (mt) cc_final: 0.8359 (pp) REVERT: B 133 LYS cc_start: 0.8569 (mttt) cc_final: 0.8352 (mttm) REVERT: B 353 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8430 (mtmm) REVERT: B 394 ASP cc_start: 0.8683 (m-30) cc_final: 0.8269 (m-30) REVERT: B 498 THR cc_start: 0.8915 (m) cc_final: 0.8469 (p) REVERT: B 531 GLN cc_start: 0.8477 (pm20) cc_final: 0.8058 (pp30) REVERT: B 566 LEU cc_start: 0.8628 (tp) cc_final: 0.8396 (tp) REVERT: B 598 GLU cc_start: 0.8907 (tp30) cc_final: 0.8342 (tm-30) REVERT: B 847 ASP cc_start: 0.8506 (m-30) cc_final: 0.8261 (m-30) REVERT: B 914 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8096 (ttpp) REVERT: B 958 GLN cc_start: 0.8562 (tt0) cc_final: 0.7928 (tm-30) REVERT: B 1057 LYS cc_start: 0.8899 (mttt) cc_final: 0.8680 (tttp) REVERT: B 1072 MET cc_start: 0.9249 (mtp) cc_final: 0.9043 (mtp) REVERT: B 1082 MET cc_start: 0.7852 (tpp) cc_final: 0.7428 (tpp) REVERT: B 1120 GLU cc_start: 0.8369 (tt0) cc_final: 0.8103 (pt0) REVERT: B 1132 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7640 (tm-30) REVERT: B 1136 ASP cc_start: 0.8969 (m-30) cc_final: 0.7558 (m-30) REVERT: B 1223 ASP cc_start: 0.7431 (t0) cc_final: 0.6981 (t0) REVERT: C 9 LYS cc_start: 0.8792 (tptm) cc_final: 0.8206 (tptt) REVERT: C 50 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8146 (mt-10) REVERT: C 177 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8337 (mt-10) REVERT: C 207 CYS cc_start: 0.8991 (m) cc_final: 0.8546 (m) REVERT: D 1 MET cc_start: 0.2304 (ptm) cc_final: 0.2003 (ptm) REVERT: D 8 PHE cc_start: 0.7221 (m-80) cc_final: 0.6982 (m-80) REVERT: D 38 ILE cc_start: 0.9107 (mt) cc_final: 0.8723 (mm) REVERT: D 58 VAL cc_start: 0.8675 (t) cc_final: 0.8177 (p) REVERT: D 61 GLU cc_start: 0.9111 (pt0) cc_final: 0.8730 (pp20) REVERT: D 65 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8318 (mm-30) REVERT: D 127 ASP cc_start: 0.6703 (m-30) cc_final: 0.6383 (m-30) REVERT: D 139 LYS cc_start: 0.8593 (tttt) cc_final: 0.8084 (tppt) REVERT: D 141 LEU cc_start: 0.9167 (tp) cc_final: 0.8951 (tp) REVERT: D 142 LYS cc_start: 0.8030 (tttt) cc_final: 0.7657 (mtmt) REVERT: D 150 ASN cc_start: 0.7392 (m-40) cc_final: 0.7159 (m-40) REVERT: E 33 GLU cc_start: 0.9022 (tt0) cc_final: 0.8659 (tm-30) REVERT: E 177 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8160 (mtm-85) REVERT: E 203 GLU cc_start: 0.9113 (pt0) cc_final: 0.8810 (pp20) REVERT: F 77 ASP cc_start: 0.8642 (m-30) cc_final: 0.8222 (p0) REVERT: F 89 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8305 (mt-10) REVERT: F 104 ASN cc_start: 0.8731 (m-40) cc_final: 0.8483 (t0) REVERT: F 112 GLU cc_start: 0.8828 (mp0) cc_final: 0.8581 (mp0) REVERT: F 116 ASP cc_start: 0.8789 (t0) cc_final: 0.8448 (t0) REVERT: G 21 ARG cc_start: 0.8738 (mtt180) cc_final: 0.8305 (ttm-80) REVERT: G 24 GLN cc_start: 0.8475 (mt0) cc_final: 0.7935 (tm-30) REVERT: G 50 ASP cc_start: 0.7443 (t0) cc_final: 0.7209 (t0) REVERT: G 53 ASN cc_start: 0.9203 (m-40) cc_final: 0.8757 (t0) REVERT: G 58 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7091 (mtt90) REVERT: H 8 ASP cc_start: 0.8276 (t0) cc_final: 0.7088 (t0) REVERT: H 14 GLU cc_start: 0.8862 (tt0) cc_final: 0.8476 (tp30) REVERT: H 27 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7744 (mp0) REVERT: H 41 ASP cc_start: 0.8825 (m-30) cc_final: 0.8059 (m-30) REVERT: H 109 LYS cc_start: 0.9092 (mppt) cc_final: 0.8869 (tptp) REVERT: H 110 ASP cc_start: 0.8919 (p0) cc_final: 0.8697 (m-30) REVERT: H 122 LEU cc_start: 0.8847 (mt) cc_final: 0.8412 (mp) REVERT: H 126 GLU cc_start: 0.8601 (tt0) cc_final: 0.8370 (tt0) REVERT: H 128 ASN cc_start: 0.8938 (t0) cc_final: 0.8543 (t0) REVERT: H 136 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8735 (mmmm) REVERT: H 137 GLN cc_start: 0.9048 (tt0) cc_final: 0.8741 (tm-30) REVERT: I 15 TYR cc_start: 0.6314 (m-80) cc_final: 0.5663 (m-80) REVERT: J 1 MET cc_start: 0.8784 (mtm) cc_final: 0.8508 (mtp) REVERT: J 27 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7807 (tm-30) REVERT: J 31 ASP cc_start: 0.7979 (p0) cc_final: 0.7778 (p0) REVERT: K 22 ASP cc_start: 0.8330 (m-30) cc_final: 0.7782 (m-30) REVERT: K 26 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8361 (mtmm) REVERT: K 32 VAL cc_start: 0.8688 (t) cc_final: 0.8374 (p) REVERT: K 49 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8714 (tp30) REVERT: K 79 GLU cc_start: 0.9185 (tt0) cc_final: 0.8981 (tp30) REVERT: L 44 ASP cc_start: 0.8100 (t70) cc_final: 0.7717 (m-30) REVERT: L 54 ARG cc_start: 0.6704 (mtt-85) cc_final: 0.6491 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 774 average time/residue: 0.2523 time to fit residues: 303.0593 Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 83 HIS A 109 HIS A 339 ASN A 358 ASN A 445 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN A 972 HIS ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 110 HIS B 357 GLN B 469 GLN B 573 GLN ** B 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS G 153 GLN I 90 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067225 restraints weight = 75097.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.069500 restraints weight = 36048.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070978 restraints weight = 22843.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071889 restraints weight = 17250.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.072378 restraints weight = 14661.940| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 33905 Z= 0.254 Angle : 0.675 12.307 46198 Z= 0.353 Chirality : 0.047 0.248 5190 Planarity : 0.005 0.064 5630 Dihedral : 16.994 154.267 5346 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 1.75 % Allowed : 7.83 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.44 (0.14), residues: 3854 helix: 1.52 (0.14), residues: 1322 sheet: 0.08 (0.21), residues: 620 loop : -0.47 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 155 TYR 0.031 0.002 TYR E 112 PHE 0.026 0.002 PHE G 2 TRP 0.012 0.001 TRP B 561 HIS 0.011 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (33873) covalent geometry : angle 0.66449 / 0.35 (46153) hydrogen bonds : bond 0.04839 / 3.24 ( 1436) hydrogen bonds : angle 5.28270 / 3.81 ( 3985) metal coordination : bond 0.01005 / 0.65 ( 32) metal coordination : angle 3.86084 / 2.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 482 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9015 (tpp) cc_final: 0.8754 (tpp) REVERT: A 218 ASP cc_start: 0.8893 (m-30) cc_final: 0.8656 (m-30) REVERT: A 277 GLU cc_start: 0.9099 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 445 ASN cc_start: 0.9119 (t0) cc_final: 0.8845 (t0) REVERT: A 453 MET cc_start: 0.8869 (mpp) cc_final: 0.8083 (mtm) REVERT: A 456 MET cc_start: 0.9233 (mtm) cc_final: 0.8927 (mtp) REVERT: A 487 MET cc_start: 0.8635 (mtp) cc_final: 0.8414 (mtp) REVERT: A 728 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8864 (mtmm) REVERT: A 847 ASP cc_start: 0.8138 (p0) cc_final: 0.7618 (p0) REVERT: A 873 MET cc_start: 0.8977 (mmp) cc_final: 0.8381 (mmp) REVERT: A 919 ILE cc_start: 0.8888 (mm) cc_final: 0.8640 (pt) REVERT: A 1268 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 1280 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 1307 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8450 (mt-10) REVERT: A 1450 LEU cc_start: 0.9479 (tp) cc_final: 0.9277 (tt) REVERT: B 353 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8690 (mtmm) REVERT: B 566 LEU cc_start: 0.8928 (tp) cc_final: 0.8655 (tp) REVERT: B 598 GLU cc_start: 0.8731 (tp30) cc_final: 0.8270 (tm-30) REVERT: B 839 MET cc_start: 0.8395 (ptp) cc_final: 0.8193 (ptp) REVERT: B 847 ASP cc_start: 0.8513 (m-30) cc_final: 0.8305 (m-30) REVERT: B 914 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8542 (ttpp) REVERT: B 958 GLN cc_start: 0.8628 (tt0) cc_final: 0.8416 (tm-30) REVERT: B 1010 LEU cc_start: 0.9452 (tp) cc_final: 0.9158 (mt) REVERT: B 1132 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7624 (tm-30) REVERT: B 1136 ASP cc_start: 0.8513 (m-30) cc_final: 0.6388 (m-30) REVERT: B 1223 ASP cc_start: 0.7411 (t0) cc_final: 0.7201 (t0) REVERT: C 9 LYS cc_start: 0.9100 (tptm) cc_final: 0.8675 (tptt) REVERT: C 207 CYS cc_start: 0.8374 (m) cc_final: 0.8151 (m) REVERT: D 1 MET cc_start: 0.2048 (ptm) cc_final: 0.1690 (ptm) REVERT: D 58 VAL cc_start: 0.8957 (t) cc_final: 0.8517 (m) REVERT: D 61 GLU cc_start: 0.8904 (pt0) cc_final: 0.8395 (pp20) REVERT: D 65 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8151 (mm-30) REVERT: D 67 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7657 (tpp80) REVERT: D 127 ASP cc_start: 0.6977 (m-30) cc_final: 0.6679 (m-30) REVERT: D 138 ASN cc_start: 0.8512 (m110) cc_final: 0.7985 (m110) REVERT: D 139 LYS cc_start: 0.8791 (tttt) cc_final: 0.8443 (tppt) REVERT: D 141 LEU cc_start: 0.9303 (tp) cc_final: 0.9074 (tp) REVERT: D 142 LYS cc_start: 0.7841 (tttt) cc_final: 0.7589 (mtmm) REVERT: D 143 ASN cc_start: 0.8226 (m110) cc_final: 0.7889 (m110) REVERT: E 32 GLN cc_start: 0.9244 (tp40) cc_final: 0.9003 (tp40) REVERT: F 89 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8365 (mt-10) REVERT: G 24 GLN cc_start: 0.8573 (mt0) cc_final: 0.8213 (tm-30) REVERT: G 50 ASP cc_start: 0.8019 (t0) cc_final: 0.7713 (t0) REVERT: G 53 ASN cc_start: 0.9067 (m-40) cc_final: 0.8562 (t0) REVERT: G 144 ARG cc_start: 0.7017 (ttm-80) cc_final: 0.6103 (ttm-80) REVERT: H 37 LYS cc_start: 0.9025 (ptpt) cc_final: 0.8576 (ptpp) REVERT: K 64 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8090 (mt-10) outliers start: 60 outliers final: 33 residues processed: 519 average time/residue: 0.2314 time to fit residues: 193.6498 Evaluate side-chains 446 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 410 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 373 optimal weight: 0.0870 chunk 22 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 304 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 548 ASN A 757 ASN B 469 GLN B 484 ASN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 153 GLN G 158 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.069149 restraints weight = 74418.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.071466 restraints weight = 35206.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.072986 restraints weight = 22184.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073902 restraints weight = 16674.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.074401 restraints weight = 14147.655| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33905 Z= 0.126 Angle : 0.575 11.957 46198 Z= 0.303 Chirality : 0.044 0.247 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.859 154.536 5346 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 1.69 % Allowed : 9.84 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.51 (0.14), residues: 3854 helix: 1.60 (0.15), residues: 1330 sheet: 0.07 (0.21), residues: 600 loop : -0.43 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1222 TYR 0.027 0.001 TYR E 112 PHE 0.021 0.001 PHE A 219 TRP 0.007 0.001 TRP F 146 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (33873) covalent geometry : angle 0.56624 / 0.30 (46153) hydrogen bonds : bond 0.04012 / 2.69 ( 1436) hydrogen bonds : angle 4.85046 / 3.51 ( 3985) metal coordination : bond 0.00543 / 0.34 ( 32) metal coordination : angle 3.20670 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 481 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8085 (mtt) cc_final: 0.7846 (mtt) REVERT: A 122 MET cc_start: 0.9035 (tpp) cc_final: 0.8738 (tpp) REVERT: A 146 MET cc_start: 0.8197 (mmm) cc_final: 0.7706 (mmp) REVERT: A 218 ASP cc_start: 0.8887 (m-30) cc_final: 0.8657 (m-30) REVERT: A 277 GLU cc_start: 0.9093 (tt0) cc_final: 0.8773 (tm-30) REVERT: A 453 MET cc_start: 0.8881 (mpp) cc_final: 0.8051 (mtm) REVERT: A 456 MET cc_start: 0.9269 (mtm) cc_final: 0.8897 (mtp) REVERT: A 487 MET cc_start: 0.8683 (mtp) cc_final: 0.8435 (mtp) REVERT: A 698 GLN cc_start: 0.8432 (tt0) cc_final: 0.8225 (pt0) REVERT: A 728 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8834 (mtmm) REVERT: A 847 ASP cc_start: 0.8161 (p0) cc_final: 0.7643 (p0) REVERT: A 873 MET cc_start: 0.8890 (mmp) cc_final: 0.8462 (mmp) REVERT: A 919 ILE cc_start: 0.8760 (mm) cc_final: 0.8536 (pt) REVERT: A 1056 SER cc_start: 0.9170 (m) cc_final: 0.8802 (m) REVERT: A 1270 ASN cc_start: 0.8643 (t0) cc_final: 0.8209 (t0) REVERT: A 1307 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8445 (mt-10) REVERT: A 1426 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: A 1450 LEU cc_start: 0.9484 (tp) cc_final: 0.9148 (tt) REVERT: B 267 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8418 (mtp85) REVERT: B 353 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8666 (mtmm) REVERT: B 394 ASP cc_start: 0.8647 (m-30) cc_final: 0.8408 (m-30) REVERT: B 507 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8597 (mmmm) REVERT: B 561 TRP cc_start: 0.8597 (m-10) cc_final: 0.8230 (m-90) REVERT: B 566 LEU cc_start: 0.8902 (tp) cc_final: 0.8631 (tp) REVERT: B 598 GLU cc_start: 0.8736 (tp30) cc_final: 0.8287 (tm-30) REVERT: B 747 MET cc_start: 0.8958 (mmp) cc_final: 0.8646 (mmm) REVERT: B 847 ASP cc_start: 0.8528 (m-30) cc_final: 0.8312 (m-30) REVERT: B 914 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8527 (ttpp) REVERT: B 935 ARG cc_start: 0.3903 (tpm170) cc_final: 0.2286 (tpt170) REVERT: B 958 GLN cc_start: 0.8522 (tt0) cc_final: 0.8192 (tm-30) REVERT: B 1010 LEU cc_start: 0.9378 (tp) cc_final: 0.8921 (mt) REVERT: B 1072 MET cc_start: 0.8930 (mtp) cc_final: 0.8529 (mtp) REVERT: B 1132 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7339 (tm-30) REVERT: B 1136 ASP cc_start: 0.8538 (m-30) cc_final: 0.6436 (m-30) REVERT: C 9 LYS cc_start: 0.9053 (tptm) cc_final: 0.8623 (tptt) REVERT: C 207 CYS cc_start: 0.8236 (m) cc_final: 0.7989 (m) REVERT: D 1 MET cc_start: 0.2033 (ptm) cc_final: 0.1717 (ptm) REVERT: D 58 VAL cc_start: 0.8905 (t) cc_final: 0.8460 (m) REVERT: D 61 GLU cc_start: 0.8902 (pt0) cc_final: 0.8332 (pp20) REVERT: D 65 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 70 PHE cc_start: 0.7757 (t80) cc_final: 0.7388 (m-80) REVERT: D 127 ASP cc_start: 0.7040 (m-30) cc_final: 0.6665 (m-30) REVERT: D 138 ASN cc_start: 0.8384 (m110) cc_final: 0.7779 (m110) REVERT: D 139 LYS cc_start: 0.8759 (tttt) cc_final: 0.8452 (tppt) REVERT: D 143 ASN cc_start: 0.8220 (m110) cc_final: 0.7885 (m110) REVERT: D 204 ASP cc_start: 0.6351 (t0) cc_final: 0.6015 (t70) REVERT: E 50 MET cc_start: 0.8413 (ppp) cc_final: 0.8155 (ppp) REVERT: E 93 MET cc_start: 0.9010 (tpp) cc_final: 0.8657 (ttm) REVERT: F 89 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8413 (mt-10) REVERT: G 24 GLN cc_start: 0.8479 (mt0) cc_final: 0.8033 (tm-30) REVERT: G 44 TYR cc_start: 0.8724 (m-80) cc_final: 0.8509 (m-10) REVERT: G 50 ASP cc_start: 0.7955 (t0) cc_final: 0.7443 (t0) REVERT: G 144 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.5850 (ttm-80) REVERT: H 37 LYS cc_start: 0.8989 (ptpt) cc_final: 0.8502 (ptpt) REVERT: H 146 ARG cc_start: 0.8304 (ttp-170) cc_final: 0.8093 (ttm170) REVERT: I 89 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8050 (mm110) REVERT: J 29 GLU cc_start: 0.8373 (pm20) cc_final: 0.8173 (pm20) REVERT: K 61 TYR cc_start: 0.8991 (p90) cc_final: 0.8725 (p90) REVERT: K 64 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: L 37 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8125 (mtmt) outliers start: 58 outliers final: 35 residues processed: 509 average time/residue: 0.2166 time to fit residues: 178.4278 Evaluate side-chains 472 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 434 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 138 optimal weight: 0.0970 chunk 183 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 286 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 251 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 overall best weight: 1.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** 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 = 0.3441 r_free = 0.3441 target = 0.098066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069007 restraints weight = 73951.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071287 restraints weight = 34856.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.072773 restraints weight = 21909.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073671 restraints weight = 16444.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074133 restraints weight = 13938.824| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33905 Z= 0.146 Angle : 0.565 11.786 46198 Z= 0.296 Chirality : 0.044 0.248 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.857 154.426 5346 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 1.69 % Allowed : 10.89 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.49 (0.14), residues: 3854 helix: 1.61 (0.15), residues: 1338 sheet: 0.03 (0.21), residues: 586 loop : -0.46 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1222 TYR 0.026 0.001 TYR E 112 PHE 0.021 0.001 PHE A 219 TRP 0.009 0.001 TRP B 561 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (33873) covalent geometry : angle 0.55573 / 0.30 (46153) hydrogen bonds : bond 0.03707 / 2.50 ( 1436) hydrogen bonds : angle 4.71524 / 3.41 ( 3985) metal coordination : bond 0.00766 / 0.46 ( 32) metal coordination : angle 3.26828 / 2.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 449 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9055 (tpp) cc_final: 0.8721 (tpp) REVERT: A 146 MET cc_start: 0.8246 (mmm) cc_final: 0.7777 (mmp) REVERT: A 218 ASP cc_start: 0.8905 (m-30) cc_final: 0.8673 (m-30) REVERT: A 277 GLU cc_start: 0.9104 (tt0) cc_final: 0.8780 (tm-30) REVERT: A 453 MET cc_start: 0.8875 (mpp) cc_final: 0.8061 (mtm) REVERT: A 455 MET cc_start: 0.8387 (mtp) cc_final: 0.8069 (ttm) REVERT: A 456 MET cc_start: 0.9239 (mtm) cc_final: 0.8892 (mtp) REVERT: A 487 MET cc_start: 0.8705 (mtp) cc_final: 0.8462 (mtp) REVERT: A 728 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8835 (mtmm) REVERT: A 847 ASP cc_start: 0.8184 (p0) cc_final: 0.7715 (p0) REVERT: A 919 ILE cc_start: 0.8753 (mm) cc_final: 0.8516 (pt) REVERT: A 1202 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8799 (tpt) REVERT: A 1285 MET cc_start: 0.8222 (mmm) cc_final: 0.7787 (tpp) REVERT: A 1307 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8466 (mt-10) REVERT: A 1426 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: A 1450 LEU cc_start: 0.9468 (tp) cc_final: 0.9226 (tt) REVERT: B 61 ASP cc_start: 0.8667 (m-30) cc_final: 0.8038 (t0) REVERT: B 353 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8662 (mtmm) REVERT: B 394 ASP cc_start: 0.8647 (m-30) cc_final: 0.8417 (m-30) REVERT: B 561 TRP cc_start: 0.8593 (m-10) cc_final: 0.8247 (m-90) REVERT: B 566 LEU cc_start: 0.8936 (tp) cc_final: 0.8639 (tp) REVERT: B 598 GLU cc_start: 0.8765 (tp30) cc_final: 0.8257 (tm-30) REVERT: B 747 MET cc_start: 0.9036 (mmp) cc_final: 0.8744 (mmm) REVERT: B 914 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8651 (ttpp) REVERT: B 935 ARG cc_start: 0.4062 (tpm170) cc_final: 0.2393 (tpt170) REVERT: B 958 GLN cc_start: 0.8519 (tt0) cc_final: 0.8169 (tm-30) REVERT: B 1132 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7392 (tm-30) REVERT: B 1136 ASP cc_start: 0.8551 (m-30) cc_final: 0.6570 (m-30) REVERT: C 9 LYS cc_start: 0.9067 (tptm) cc_final: 0.8624 (tptt) REVERT: C 207 CYS cc_start: 0.8256 (m) cc_final: 0.7983 (m) REVERT: D 1 MET cc_start: 0.1967 (ptm) cc_final: 0.1705 (ptm) REVERT: D 58 VAL cc_start: 0.8908 (t) cc_final: 0.8453 (m) REVERT: D 61 GLU cc_start: 0.8884 (pt0) cc_final: 0.8291 (pp20) REVERT: D 65 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 70 PHE cc_start: 0.7736 (t80) cc_final: 0.7443 (m-80) REVERT: D 139 LYS cc_start: 0.8642 (tttt) cc_final: 0.8419 (pttm) REVERT: E 50 MET cc_start: 0.8534 (ppp) cc_final: 0.8145 (ppp) REVERT: F 89 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8358 (mt-10) REVERT: F 104 ASN cc_start: 0.8867 (t0) cc_final: 0.8503 (t0) REVERT: G 44 TYR cc_start: 0.8683 (m-80) cc_final: 0.8461 (m-10) REVERT: G 50 ASP cc_start: 0.8006 (t0) cc_final: 0.7685 (t0) REVERT: G 53 ASN cc_start: 0.8965 (m-40) cc_final: 0.8437 (t0) REVERT: H 37 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8550 (ptpp) REVERT: H 146 ARG cc_start: 0.8332 (ttp-170) cc_final: 0.8087 (ttm170) REVERT: I 89 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8022 (mm110) REVERT: K 22 ASP cc_start: 0.8309 (m-30) cc_final: 0.8100 (m-30) REVERT: K 36 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8335 (mm-30) REVERT: K 64 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8075 (mt-10) outliers start: 58 outliers final: 38 residues processed: 478 average time/residue: 0.2135 time to fit residues: 165.7274 Evaluate side-chains 456 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 415 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS B 469 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** 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 = 0.3460 r_free = 0.3460 target = 0.099249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.070148 restraints weight = 74093.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072484 restraints weight = 34737.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073992 restraints weight = 21668.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.074933 restraints weight = 16243.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075476 restraints weight = 13698.457| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33905 Z= 0.109 Angle : 0.542 10.670 46198 Z= 0.285 Chirality : 0.043 0.246 5190 Planarity : 0.004 0.054 5630 Dihedral : 16.814 154.373 5346 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 1.66 % Allowed : 11.36 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.54 (0.14), residues: 3854 helix: 1.67 (0.15), residues: 1343 sheet: 0.00 (0.21), residues: 588 loop : -0.43 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 209 TYR 0.025 0.001 TYR E 112 PHE 0.023 0.001 PHE A 219 TRP 0.008 0.001 TRP B 561 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (33873) covalent geometry : angle 0.53525 / 0.28 (46153) hydrogen bonds : bond 0.03410 / 2.30 ( 1436) hydrogen bonds : angle 4.54598 / 3.29 ( 3985) metal coordination : bond 0.00491 / 0.31 ( 32) metal coordination : angle 2.84241 / 2.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 469 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9058 (tpp) cc_final: 0.8719 (tpp) REVERT: A 146 MET cc_start: 0.8241 (mmm) cc_final: 0.7784 (mmp) REVERT: A 218 ASP cc_start: 0.8928 (m-30) cc_final: 0.8723 (m-30) REVERT: A 277 GLU cc_start: 0.9100 (tt0) cc_final: 0.8775 (tm-30) REVERT: A 453 MET cc_start: 0.8846 (mpp) cc_final: 0.8465 (mtm) REVERT: A 456 MET cc_start: 0.9204 (mtm) cc_final: 0.8848 (mtp) REVERT: A 487 MET cc_start: 0.8644 (mtp) cc_final: 0.8382 (mtp) REVERT: A 728 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8798 (mtmm) REVERT: A 847 ASP cc_start: 0.8148 (p0) cc_final: 0.7758 (p0) REVERT: A 873 MET cc_start: 0.8821 (mmp) cc_final: 0.8176 (mmp) REVERT: A 919 ILE cc_start: 0.8677 (mm) cc_final: 0.8456 (pt) REVERT: A 1209 MET cc_start: 0.8700 (mmm) cc_final: 0.8447 (mmm) REVERT: A 1285 MET cc_start: 0.8245 (mmm) cc_final: 0.7805 (tpp) REVERT: A 1307 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8435 (mt-10) REVERT: A 1411 GLU cc_start: 0.8417 (tp30) cc_final: 0.7969 (tp30) REVERT: A 1426 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: B 61 ASP cc_start: 0.8598 (m-30) cc_final: 0.7977 (t0) REVERT: B 353 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8661 (mtmm) REVERT: B 394 ASP cc_start: 0.8622 (m-30) cc_final: 0.8402 (m-30) REVERT: B 531 GLN cc_start: 0.7364 (pp30) cc_final: 0.7046 (tm-30) REVERT: B 561 TRP cc_start: 0.8541 (m-10) cc_final: 0.8203 (m-90) REVERT: B 566 LEU cc_start: 0.8889 (tp) cc_final: 0.8573 (tp) REVERT: B 598 GLU cc_start: 0.8765 (tp30) cc_final: 0.8289 (tm-30) REVERT: B 747 MET cc_start: 0.9067 (mmp) cc_final: 0.8795 (mmm) REVERT: B 861 ASP cc_start: 0.8392 (t0) cc_final: 0.8055 (m-30) REVERT: B 914 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8675 (ttpp) REVERT: B 935 ARG cc_start: 0.4251 (tpm170) cc_final: 0.2637 (tpt170) REVERT: B 958 GLN cc_start: 0.8472 (tt0) cc_final: 0.8154 (tm-30) REVERT: B 1072 MET cc_start: 0.8993 (mtp) cc_final: 0.8571 (mtp) REVERT: B 1132 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7400 (tm-30) REVERT: B 1136 ASP cc_start: 0.8567 (m-30) cc_final: 0.6588 (m-30) REVERT: C 9 LYS cc_start: 0.9047 (tptm) cc_final: 0.8607 (tptt) REVERT: D 1 MET cc_start: 0.2020 (ptm) cc_final: 0.1733 (ptm) REVERT: D 58 VAL cc_start: 0.8895 (t) cc_final: 0.8429 (m) REVERT: D 61 GLU cc_start: 0.8876 (pt0) cc_final: 0.8306 (pp20) REVERT: D 65 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8220 (mm-30) REVERT: D 70 PHE cc_start: 0.7740 (t80) cc_final: 0.7410 (m-80) REVERT: D 139 LYS cc_start: 0.8596 (tttt) cc_final: 0.8387 (pttm) REVERT: E 50 MET cc_start: 0.8573 (ppp) cc_final: 0.8177 (ppp) REVERT: F 89 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8418 (mt-10) REVERT: F 104 ASN cc_start: 0.8811 (t0) cc_final: 0.8471 (t0) REVERT: F 112 GLU cc_start: 0.8445 (mp0) cc_final: 0.8238 (mp0) REVERT: G 24 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7833 (tm-30) REVERT: G 44 TYR cc_start: 0.8682 (m-80) cc_final: 0.8455 (m-10) REVERT: G 50 ASP cc_start: 0.7876 (t0) cc_final: 0.7578 (t0) REVERT: G 53 ASN cc_start: 0.8947 (m-40) cc_final: 0.8449 (t0) REVERT: G 75 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7385 (ttt180) REVERT: G 144 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.5803 (ttm-80) REVERT: H 27 GLU cc_start: 0.7917 (pm20) cc_final: 0.7653 (pm20) REVERT: H 37 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8482 (ptpt) REVERT: H 146 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.8066 (ttm170) REVERT: J 16 ASP cc_start: 0.8695 (p0) cc_final: 0.8386 (p0) REVERT: K 22 ASP cc_start: 0.8255 (m-30) cc_final: 0.8043 (m-30) REVERT: K 36 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8368 (mm-30) REVERT: K 64 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: L 37 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8102 (mtmt) outliers start: 57 outliers final: 33 residues processed: 498 average time/residue: 0.2178 time to fit residues: 177.5099 Evaluate side-chains 460 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 424 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** K 2 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.097430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.068819 restraints weight = 74741.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.071250 restraints weight = 35080.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.072140 restraints weight = 20194.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.072311 restraints weight = 17499.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.072405 restraints weight = 16539.419| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33905 Z= 0.196 Angle : 0.580 11.404 46198 Z= 0.302 Chirality : 0.044 0.248 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.866 155.257 5346 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 1.92 % Allowed : 12.20 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.51 (0.14), residues: 3854 helix: 1.69 (0.15), residues: 1336 sheet: -0.08 (0.21), residues: 603 loop : -0.44 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 209 TYR 0.028 0.001 TYR E 112 PHE 0.020 0.001 PHE A 219 TRP 0.011 0.001 TRP B 561 HIS 0.011 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (33873) covalent geometry : angle 0.57156 / 0.30 (46153) hydrogen bonds : bond 0.03547 / 2.41 ( 1436) hydrogen bonds : angle 4.59359 / 3.33 ( 3985) metal coordination : bond 0.00822 / 0.53 ( 32) metal coordination : angle 3.26307 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 421 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8960 (m-30) cc_final: 0.8696 (m-30) REVERT: A 277 GLU cc_start: 0.9140 (tt0) cc_final: 0.8818 (tm-30) REVERT: A 304 MET cc_start: 0.9241 (tpp) cc_final: 0.8554 (mtp) REVERT: A 453 MET cc_start: 0.8866 (mpp) cc_final: 0.8173 (mtm) REVERT: A 456 MET cc_start: 0.9243 (mtm) cc_final: 0.8892 (mtp) REVERT: A 487 MET cc_start: 0.8647 (mtp) cc_final: 0.8389 (mtp) REVERT: A 728 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8808 (mtmm) REVERT: A 847 ASP cc_start: 0.8077 (p0) cc_final: 0.7676 (p0) REVERT: A 873 MET cc_start: 0.8832 (mmp) cc_final: 0.8248 (mmp) REVERT: A 919 ILE cc_start: 0.8687 (mm) cc_final: 0.8454 (pt) REVERT: A 1209 MET cc_start: 0.8718 (mmm) cc_final: 0.8449 (mmm) REVERT: A 1307 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8581 (mt-10) REVERT: A 1411 GLU cc_start: 0.8455 (tp30) cc_final: 0.8004 (tp30) REVERT: A 1426 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: B 353 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8610 (mtmm) REVERT: B 394 ASP cc_start: 0.8726 (m-30) cc_final: 0.8477 (m-30) REVERT: B 561 TRP cc_start: 0.8546 (m-10) cc_final: 0.8136 (m-90) REVERT: B 598 GLU cc_start: 0.8780 (tp30) cc_final: 0.8258 (tm-30) REVERT: B 747 MET cc_start: 0.9137 (mmp) cc_final: 0.8828 (mmm) REVERT: B 861 ASP cc_start: 0.8438 (t0) cc_final: 0.8020 (m-30) REVERT: B 914 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8666 (ttpp) REVERT: B 935 ARG cc_start: 0.4181 (tpm170) cc_final: 0.2701 (tpt170) REVERT: B 958 GLN cc_start: 0.8559 (tt0) cc_final: 0.8124 (tm-30) REVERT: B 1072 MET cc_start: 0.8994 (mtp) cc_final: 0.8553 (mtp) REVERT: B 1132 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7469 (tm-30) REVERT: B 1136 ASP cc_start: 0.8539 (m-30) cc_final: 0.6569 (m-30) REVERT: C 9 LYS cc_start: 0.9080 (tptm) cc_final: 0.8652 (tptt) REVERT: D 1 MET cc_start: 0.1894 (ptm) cc_final: 0.1679 (ptm) REVERT: D 61 GLU cc_start: 0.8903 (pt0) cc_final: 0.8334 (pp20) REVERT: D 65 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8278 (mm-30) REVERT: D 139 LYS cc_start: 0.8620 (tttt) cc_final: 0.8409 (pttm) REVERT: E 50 MET cc_start: 0.8701 (ppp) cc_final: 0.8285 (ppp) REVERT: F 85 MET cc_start: 0.9171 (tmm) cc_final: 0.8933 (ttp) REVERT: F 89 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8361 (mt-10) REVERT: F 104 ASN cc_start: 0.8787 (t0) cc_final: 0.8450 (t0) REVERT: F 112 GLU cc_start: 0.8520 (mp0) cc_final: 0.8301 (mp0) REVERT: G 24 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7855 (tm-30) REVERT: G 44 TYR cc_start: 0.8689 (m-80) cc_final: 0.8444 (m-10) REVERT: G 50 ASP cc_start: 0.7890 (t0) cc_final: 0.7592 (t0) REVERT: G 53 ASN cc_start: 0.8971 (m-40) cc_final: 0.8538 (t0) REVERT: G 75 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7422 (ttt180) REVERT: G 144 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6241 (ttm-80) REVERT: H 37 LYS cc_start: 0.8959 (ptpt) cc_final: 0.8639 (ptpp) REVERT: H 126 GLU cc_start: 0.8478 (tt0) cc_final: 0.8223 (tt0) REVERT: H 130 ARG cc_start: 0.9008 (mtm180) cc_final: 0.8617 (ptp90) REVERT: H 146 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8104 (ttm170) REVERT: I 89 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8056 (mm110) REVERT: I 99 LEU cc_start: 0.7839 (mt) cc_final: 0.7576 (mm) REVERT: K 36 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8353 (mm-30) REVERT: K 64 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: L 37 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8059 (mtmt) outliers start: 66 outliers final: 48 residues processed: 455 average time/residue: 0.2207 time to fit residues: 164.1326 Evaluate side-chains 448 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 397 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 200 optimal weight: 0.0980 chunk 306 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 354 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069161 restraints weight = 74645.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071444 restraints weight = 35324.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.072920 restraints weight = 22164.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073832 restraints weight = 16685.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074319 restraints weight = 14109.720| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33905 Z= 0.148 Angle : 0.559 11.306 46198 Z= 0.292 Chirality : 0.043 0.247 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.864 155.839 5346 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.82 % Rotamer: Outliers : 1.72 % Allowed : 12.93 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.56 (0.14), residues: 3854 helix: 1.72 (0.15), residues: 1335 sheet: -0.08 (0.22), residues: 567 loop : -0.40 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 209 TYR 0.035 0.001 TYR E 112 PHE 0.031 0.001 PHE D 70 TRP 0.012 0.001 TRP B 561 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (33873) covalent geometry : angle 0.55074 / 0.29 (46153) hydrogen bonds : bond 0.03378 / 2.28 ( 1436) hydrogen bonds : angle 4.47606 / 3.24 ( 3985) metal coordination : bond 0.00598 / 0.39 ( 32) metal coordination : angle 3.08478 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 416 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8898 (m-30) cc_final: 0.8658 (m-30) REVERT: A 277 GLU cc_start: 0.9080 (tt0) cc_final: 0.8807 (tm-30) REVERT: A 304 MET cc_start: 0.9244 (tpp) cc_final: 0.8564 (mtp) REVERT: A 453 MET cc_start: 0.8872 (mpp) cc_final: 0.8046 (mtm) REVERT: A 456 MET cc_start: 0.9231 (mtm) cc_final: 0.8861 (mtp) REVERT: A 487 MET cc_start: 0.8588 (mtp) cc_final: 0.8314 (mtp) REVERT: A 728 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8799 (mtmm) REVERT: A 847 ASP cc_start: 0.8055 (p0) cc_final: 0.7685 (p0) REVERT: A 873 MET cc_start: 0.8850 (mmp) cc_final: 0.8259 (mmp) REVERT: A 919 ILE cc_start: 0.8684 (mm) cc_final: 0.8467 (pt) REVERT: A 1307 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8585 (mt-10) REVERT: A 1317 MET cc_start: 0.9354 (ptt) cc_final: 0.9118 (ttp) REVERT: A 1411 GLU cc_start: 0.8425 (tp30) cc_final: 0.7960 (tp30) REVERT: A 1426 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: B 96 TYR cc_start: 0.8093 (m-80) cc_final: 0.7867 (m-10) REVERT: B 298 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9199 (mt) REVERT: B 353 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8657 (mtmm) REVERT: B 394 ASP cc_start: 0.8620 (m-30) cc_final: 0.8360 (m-30) REVERT: B 561 TRP cc_start: 0.8572 (m-10) cc_final: 0.8163 (m-90) REVERT: B 598 GLU cc_start: 0.8781 (tp30) cc_final: 0.8250 (tm-30) REVERT: B 747 MET cc_start: 0.9181 (mmp) cc_final: 0.8800 (mmm) REVERT: B 861 ASP cc_start: 0.8398 (t0) cc_final: 0.8069 (m-30) REVERT: B 914 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8694 (ttpp) REVERT: B 935 ARG cc_start: 0.4370 (tpm170) cc_final: 0.2886 (tpt170) REVERT: B 958 GLN cc_start: 0.8495 (tt0) cc_final: 0.8170 (tm-30) REVERT: B 1072 MET cc_start: 0.9002 (mtp) cc_final: 0.8544 (mtp) REVERT: B 1132 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7419 (tm-30) REVERT: B 1136 ASP cc_start: 0.8548 (m-30) cc_final: 0.6567 (m-30) REVERT: C 9 LYS cc_start: 0.9062 (tptm) cc_final: 0.8651 (tptt) REVERT: C 84 ARG cc_start: 0.8580 (ptt-90) cc_final: 0.8342 (ptt-90) REVERT: D 58 VAL cc_start: 0.8906 (t) cc_final: 0.8426 (m) REVERT: D 61 GLU cc_start: 0.8897 (pt0) cc_final: 0.8327 (pp20) REVERT: D 65 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8264 (mm-30) REVERT: D 139 LYS cc_start: 0.8566 (tttt) cc_final: 0.8340 (pttm) REVERT: E 50 MET cc_start: 0.8592 (ppp) cc_final: 0.8191 (ppp) REVERT: F 85 MET cc_start: 0.9181 (tmm) cc_final: 0.8874 (ttp) REVERT: F 89 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8326 (mt-10) REVERT: F 104 ASN cc_start: 0.8774 (t0) cc_final: 0.8443 (t0) REVERT: G 24 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7862 (tm-30) REVERT: G 44 TYR cc_start: 0.8689 (m-80) cc_final: 0.8448 (m-10) REVERT: G 50 ASP cc_start: 0.7933 (t0) cc_final: 0.7564 (t0) REVERT: G 75 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7400 (ttt180) REVERT: G 144 ARG cc_start: 0.7010 (ttm-80) cc_final: 0.5880 (ttm-80) REVERT: H 37 LYS cc_start: 0.8958 (ptpt) cc_final: 0.8615 (ptpp) REVERT: H 126 GLU cc_start: 0.8445 (tt0) cc_final: 0.8201 (tt0) REVERT: H 130 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8471 (ptp90) REVERT: H 146 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8070 (ttm170) REVERT: K 36 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8338 (mm-30) REVERT: K 64 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: L 37 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8106 (mtmt) outliers start: 59 outliers final: 47 residues processed: 449 average time/residue: 0.2226 time to fit residues: 162.1887 Evaluate side-chains 456 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 405 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.2980 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 2 ASN ** 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 = 0.3409 r_free = 0.3409 target = 0.096234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.067186 restraints weight = 74985.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.069425 restraints weight = 35995.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.070875 restraints weight = 22752.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071750 restraints weight = 17235.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072291 restraints weight = 14642.684| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 33905 Z= 0.229 Angle : 0.611 12.201 46198 Z= 0.315 Chirality : 0.044 0.294 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.940 157.125 5346 Min Nonbonded Distance : 1.044 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 1.83 % Allowed : 13.25 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.48 (0.14), residues: 3854 helix: 1.69 (0.15), residues: 1319 sheet: -0.15 (0.22), residues: 556 loop : -0.44 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1366 TYR 0.035 0.002 TYR E 112 PHE 0.020 0.002 PHE A 219 TRP 0.015 0.001 TRP B 561 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (33873) covalent geometry : angle 0.60097 / 0.31 (46153) hydrogen bonds : bond 0.03660 / 2.48 ( 1436) hydrogen bonds : angle 4.59487 / 3.33 ( 3985) metal coordination : bond 0.00959 / 0.63 ( 32) metal coordination : angle 3.51469 / 2.63 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 404 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9080 (tpp) cc_final: 0.8766 (tpt) REVERT: A 218 ASP cc_start: 0.8965 (m-30) cc_final: 0.8707 (m-30) REVERT: A 277 GLU cc_start: 0.9089 (tt0) cc_final: 0.8846 (tm-30) REVERT: A 453 MET cc_start: 0.8874 (mpp) cc_final: 0.7999 (mtm) REVERT: A 456 MET cc_start: 0.9206 (mtm) cc_final: 0.8893 (mtp) REVERT: A 728 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8839 (mtmm) REVERT: A 847 ASP cc_start: 0.8129 (p0) cc_final: 0.7686 (p0) REVERT: A 873 MET cc_start: 0.8942 (mmp) cc_final: 0.8677 (mmm) REVERT: A 919 ILE cc_start: 0.8716 (mm) cc_final: 0.8509 (pt) REVERT: A 1426 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: B 353 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8643 (mtmm) REVERT: B 394 ASP cc_start: 0.8690 (m-30) cc_final: 0.8430 (m-30) REVERT: B 561 TRP cc_start: 0.8615 (m-10) cc_final: 0.8132 (m-90) REVERT: B 598 GLU cc_start: 0.8790 (tp30) cc_final: 0.8339 (tm-30) REVERT: B 861 ASP cc_start: 0.8421 (t0) cc_final: 0.8095 (m-30) REVERT: B 914 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8704 (ttpp) REVERT: B 935 ARG cc_start: 0.4333 (tpm170) cc_final: 0.2861 (tpt170) REVERT: B 958 GLN cc_start: 0.8549 (tt0) cc_final: 0.8171 (tm-30) REVERT: B 1132 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7463 (tm-30) REVERT: B 1136 ASP cc_start: 0.8571 (m-30) cc_final: 0.6554 (m-30) REVERT: C 9 LYS cc_start: 0.9067 (tptm) cc_final: 0.8662 (tptt) REVERT: D 58 VAL cc_start: 0.8912 (t) cc_final: 0.8421 (m) REVERT: D 61 GLU cc_start: 0.8908 (pt0) cc_final: 0.8342 (pp20) REVERT: D 65 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 139 LYS cc_start: 0.8598 (tttt) cc_final: 0.8395 (pttm) REVERT: E 50 MET cc_start: 0.8631 (ppp) cc_final: 0.8190 (ppp) REVERT: F 89 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8288 (mt-10) REVERT: F 104 ASN cc_start: 0.8807 (t0) cc_final: 0.8480 (t0) REVERT: F 123 LYS cc_start: 0.9628 (tttt) cc_final: 0.9332 (ttmt) REVERT: G 24 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7836 (tm-30) REVERT: G 32 GLU cc_start: 0.8790 (tp30) cc_final: 0.8536 (tp30) REVERT: G 33 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8547 (mt-10) REVERT: G 44 TYR cc_start: 0.8722 (m-80) cc_final: 0.8514 (m-10) REVERT: G 50 ASP cc_start: 0.8020 (t0) cc_final: 0.7720 (t0) REVERT: G 75 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7464 (ttt180) REVERT: G 144 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.5947 (tpp-160) REVERT: H 128 ASN cc_start: 0.8625 (p0) cc_final: 0.8417 (p0) REVERT: I 12 ASN cc_start: 0.7064 (m-40) cc_final: 0.6835 (m-40) REVERT: I 89 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8144 (mm110) REVERT: K 36 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8393 (mm-30) REVERT: K 64 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: L 37 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8153 (mtmt) outliers start: 63 outliers final: 50 residues processed: 439 average time/residue: 0.2221 time to fit residues: 158.4077 Evaluate side-chains 449 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 396 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 6.9990 chunk 377 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN H 131 ASN ** K 2 ASN ** 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 = 0.3392 r_free = 0.3392 target = 0.095287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.066312 restraints weight = 75050.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.068518 restraints weight = 36100.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.069946 restraints weight = 22901.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070831 restraints weight = 17343.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.071338 restraints weight = 14756.541| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 33905 Z= 0.267 Angle : 0.647 13.295 46198 Z= 0.332 Chirality : 0.045 0.250 5190 Planarity : 0.004 0.057 5630 Dihedral : 17.003 158.484 5346 Min Nonbonded Distance : 1.007 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 1.95 % Allowed : 13.16 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.36 (0.14), residues: 3854 helix: 1.57 (0.15), residues: 1327 sheet: -0.20 (0.22), residues: 565 loop : -0.52 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1366 TYR 0.031 0.002 TYR E 112 PHE 0.019 0.002 PHE D 70 TRP 0.017 0.001 TRP B 561 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (33873) covalent geometry : angle 0.63582 / 0.33 (46153) hydrogen bonds : bond 0.03830 / 2.60 ( 1436) hydrogen bonds : angle 4.68389 / 3.38 ( 3985) metal coordination : bond 0.01115 / 0.74 ( 32) metal coordination : angle 3.89111 / 2.90 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 401 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9085 (tpp) cc_final: 0.8762 (tpt) REVERT: A 218 ASP cc_start: 0.8978 (m-30) cc_final: 0.8722 (m-30) REVERT: A 277 GLU cc_start: 0.9086 (tt0) cc_final: 0.8864 (tm-30) REVERT: A 453 MET cc_start: 0.8862 (mpp) cc_final: 0.7986 (mtm) REVERT: A 456 MET cc_start: 0.9210 (mtm) cc_final: 0.8915 (mtp) REVERT: A 728 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8841 (mtmm) REVERT: A 847 ASP cc_start: 0.8094 (p0) cc_final: 0.7685 (p0) REVERT: A 873 MET cc_start: 0.9045 (mmp) cc_final: 0.8735 (mmm) REVERT: A 919 ILE cc_start: 0.8705 (mm) cc_final: 0.8494 (pt) REVERT: A 1426 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 96 TYR cc_start: 0.8214 (m-80) cc_final: 0.7989 (m-10) REVERT: B 353 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8631 (mtmm) REVERT: B 561 TRP cc_start: 0.8636 (m-10) cc_final: 0.8133 (m-90) REVERT: B 598 GLU cc_start: 0.8783 (tp30) cc_final: 0.8365 (tm-30) REVERT: B 861 ASP cc_start: 0.8443 (t0) cc_final: 0.8206 (t0) REVERT: B 914 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8657 (ttpp) REVERT: B 958 GLN cc_start: 0.8591 (tt0) cc_final: 0.8232 (tm-30) REVERT: B 1072 MET cc_start: 0.9012 (mtp) cc_final: 0.8544 (mtp) REVERT: B 1132 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7456 (tm-30) REVERT: B 1136 ASP cc_start: 0.8596 (m-30) cc_final: 0.6576 (m-30) REVERT: B 1223 ASP cc_start: 0.7571 (t0) cc_final: 0.7229 (t0) REVERT: C 9 LYS cc_start: 0.9079 (tptm) cc_final: 0.8672 (tptt) REVERT: D 58 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8398 (m) REVERT: D 61 GLU cc_start: 0.8852 (pt0) cc_final: 0.8334 (pp20) REVERT: D 65 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 139 LYS cc_start: 0.8687 (tttt) cc_final: 0.8483 (pttm) REVERT: E 50 MET cc_start: 0.8629 (ppp) cc_final: 0.8186 (ppp) REVERT: F 89 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 104 ASN cc_start: 0.8811 (t0) cc_final: 0.8480 (t0) REVERT: G 24 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7839 (tm-30) REVERT: G 32 GLU cc_start: 0.8794 (tp30) cc_final: 0.8534 (tp30) REVERT: G 33 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8449 (mt-10) REVERT: G 50 ASP cc_start: 0.8048 (t0) cc_final: 0.7791 (t0) REVERT: G 75 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7496 (ttt180) REVERT: G 144 ARG cc_start: 0.6811 (ttm-80) cc_final: 0.5723 (ttm-80) REVERT: I 12 ASN cc_start: 0.7279 (m-40) cc_final: 0.7044 (m-40) REVERT: I 89 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8168 (mm110) REVERT: K 36 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8365 (mm-30) REVERT: K 64 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: L 37 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8213 (mtmt) outliers start: 67 outliers final: 55 residues processed: 437 average time/residue: 0.2204 time to fit residues: 157.2362 Evaluate side-chains 449 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.0470 chunk 268 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 314 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 321 optimal weight: 0.0050 chunk 241 optimal weight: 0.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN H 137 GLN ** K 2 ASN ** 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 = 0.3447 r_free = 0.3447 target = 0.098524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.069787 restraints weight = 74528.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.072099 restraints weight = 35051.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.073581 restraints weight = 21887.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.074497 restraints weight = 16437.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.075029 restraints weight = 13895.187| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33905 Z= 0.113 Angle : 0.575 10.520 46198 Z= 0.299 Chirality : 0.043 0.247 5190 Planarity : 0.004 0.090 5630 Dihedral : 16.872 157.909 5346 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 1.40 % Allowed : 14.15 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.57 (0.14), residues: 3854 helix: 1.81 (0.15), residues: 1316 sheet: -0.15 (0.22), residues: 566 loop : -0.42 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1366 TYR 0.031 0.001 TYR E 112 PHE 0.022 0.001 PHE A 219 TRP 0.012 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (33873) covalent geometry : angle 0.56824 / 0.30 (46153) hydrogen bonds : bond 0.03300 / 2.23 ( 1436) hydrogen bonds : angle 4.44681 / 3.20 ( 3985) metal coordination : bond 0.00459 / 0.30 ( 32) metal coordination : angle 2.94745 / 2.22 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 419 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9081 (tpp) cc_final: 0.8769 (tpt) REVERT: A 171 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7114 (mp10) REVERT: A 218 ASP cc_start: 0.8885 (m-30) cc_final: 0.8632 (m-30) REVERT: A 277 GLU cc_start: 0.9066 (tt0) cc_final: 0.8830 (tm-30) REVERT: A 453 MET cc_start: 0.8855 (mpp) cc_final: 0.7998 (mtm) REVERT: A 456 MET cc_start: 0.9236 (mtm) cc_final: 0.8918 (mtp) REVERT: A 535 THR cc_start: 0.9398 (m) cc_final: 0.9140 (p) REVERT: A 728 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8826 (mtmm) REVERT: A 757 ASN cc_start: 0.8859 (m-40) cc_final: 0.8365 (t0) REVERT: A 847 ASP cc_start: 0.8052 (p0) cc_final: 0.7696 (p0) REVERT: A 919 ILE cc_start: 0.8660 (mm) cc_final: 0.8439 (pt) REVERT: A 1202 MET cc_start: 0.9258 (tpp) cc_final: 0.9046 (tpp) REVERT: A 1426 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: B 353 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8615 (mtmm) REVERT: B 561 TRP cc_start: 0.8521 (m-10) cc_final: 0.8098 (m-90) REVERT: B 598 GLU cc_start: 0.8753 (tp30) cc_final: 0.8263 (tm-30) REVERT: B 861 ASP cc_start: 0.8356 (t0) cc_final: 0.8045 (m-30) REVERT: B 914 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8690 (ttpp) REVERT: B 958 GLN cc_start: 0.8470 (tt0) cc_final: 0.7957 (tm-30) REVERT: B 1072 MET cc_start: 0.8962 (mtp) cc_final: 0.8493 (mtp) REVERT: B 1098 MET cc_start: 0.8252 (mtm) cc_final: 0.8006 (mmt) REVERT: B 1132 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7383 (tm-30) REVERT: B 1136 ASP cc_start: 0.8517 (m-30) cc_final: 0.6423 (m-30) REVERT: B 1210 MET cc_start: 0.8686 (ttm) cc_final: 0.8441 (mtp) REVERT: C 9 LYS cc_start: 0.9029 (tptm) cc_final: 0.8689 (tptp) REVERT: C 230 MET cc_start: 0.8318 (mtp) cc_final: 0.8036 (mmm) REVERT: D 58 VAL cc_start: 0.8879 (t) cc_final: 0.8382 (m) REVERT: D 61 GLU cc_start: 0.8883 (pt0) cc_final: 0.8356 (pp20) REVERT: D 65 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 50 MET cc_start: 0.8548 (ppp) cc_final: 0.8107 (ppp) REVERT: F 104 ASN cc_start: 0.8799 (t0) cc_final: 0.8457 (t0) REVERT: G 24 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7887 (tm-30) REVERT: G 32 GLU cc_start: 0.8829 (tp30) cc_final: 0.8571 (tp30) REVERT: G 33 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8373 (mt-10) REVERT: G 50 ASP cc_start: 0.8090 (t0) cc_final: 0.7887 (t0) REVERT: G 75 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7427 (ttt180) REVERT: G 144 ARG cc_start: 0.6902 (ttm-80) cc_final: 0.5909 (tpp-160) REVERT: H 136 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8565 (ttmm) REVERT: H 138 GLU cc_start: 0.8526 (pm20) cc_final: 0.8229 (pt0) REVERT: J 1 MET cc_start: 0.8837 (mtp) cc_final: 0.8188 (mmt) REVERT: K 36 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8390 (mm-30) REVERT: K 64 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: L 28 LYS cc_start: 0.7708 (mmtm) cc_final: 0.7015 (mmtt) outliers start: 48 outliers final: 37 residues processed: 441 average time/residue: 0.2166 time to fit residues: 155.8890 Evaluate side-chains 441 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 401 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1426 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 0.0170 chunk 284 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 374 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 343 optimal weight: 0.0980 chunk 296 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 2 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.098565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.069247 restraints weight = 73979.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071559 restraints weight = 35159.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.073088 restraints weight = 22174.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.074017 restraints weight = 16627.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074514 restraints weight = 14069.989| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33905 Z= 0.110 Angle : 0.574 9.950 46198 Z= 0.297 Chirality : 0.042 0.249 5190 Planarity : 0.004 0.074 5630 Dihedral : 16.828 157.866 5346 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.16 % Rotamer: Outliers : 1.25 % Allowed : 14.41 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.59 (0.14), residues: 3854 helix: 1.82 (0.15), residues: 1318 sheet: -0.16 (0.22), residues: 568 loop : -0.39 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1366 TYR 0.030 0.001 TYR E 112 PHE 0.022 0.001 PHE A 219 TRP 0.010 0.001 TRP B 561 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (33873) covalent geometry : angle 0.56743 / 0.30 (46153) hydrogen bonds : bond 0.03242 / 2.20 ( 1436) hydrogen bonds : angle 4.40194 / 3.17 ( 3985) metal coordination : bond 0.00440 / 0.28 ( 32) metal coordination : angle 2.77596 / 2.10 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6124.19 seconds wall clock time: 106 minutes 50.94 seconds (6410.94 seconds total)