Starting phenix.real_space_refine on Sun Aug 9 10:07:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbz_54744/08_2026/9sbz_54744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbz_54744/08_2026/9sbz_54744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbz_54744/08_2026/9sbz_54744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbz_54744/08_2026/9sbz_54744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbz_54744/08_2026/9sbz_54744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbz_54744/08_2026/9sbz_54744.map" } resolution = 3.35 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= 0.034 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 8 residue(s): 0.02s 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: 21 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 105.431 70.487 95.114 1.00145.92 S ATOM 479 SG CYS A 70 104.981 66.939 93.577 1.00141.41 S ATOM 532 SG CYS A 77 102.335 69.643 93.078 1.00138.95 S ATOM 762 SG CYS A 107 80.230 76.664 135.194 1.00167.78 S ATOM 786 SG CYS A 110 81.909 73.350 135.964 1.00167.03 S ATOM 1091 SG CYS A 148 78.422 74.075 137.286 1.00180.16 S ATOM 1105 SG CYS A 167 81.407 76.034 138.681 1.00179.16 S ATOM 19603 SG CYS B1163 97.336 58.014 104.948 1.00130.05 S ATOM 19621 SG CYS B1166 95.697 61.251 105.706 1.00138.01 S ATOM 19746 SG CYS B1182 99.436 61.035 104.668 1.00146.18 S ATOM 19765 SG CYS B1185 98.246 60.033 108.183 1.00145.33 S ATOM 20753 SG CYS C 86 91.750 74.980 25.938 1.00185.31 S ATOM 20770 SG CYS C 88 93.807 77.146 28.273 1.00193.08 S ATOM 20803 SG CYS C 92 93.046 78.331 24.787 1.00159.53 S ATOM 20826 SG CYS C 95 90.237 78.164 27.403 1.00148.88 S ATOM 28411 SG CYS I 7 39.901 125.219 128.013 1.00257.60 S ATOM 28436 SG CYS I 10 43.602 124.494 127.654 1.00250.37 S ATOM 28602 SG CYS I 29 41.392 122.080 129.661 1.00252.60 S ATOM 28626 SG CYS I 32 42.223 125.400 131.069 1.00258.16 S ATOM 28953 SG CYS I 75 15.840 115.903 89.682 1.00250.58 S ATOM 28975 SG CYS I 78 15.599 119.463 88.411 1.00260.03 S ATOM 29191 SG CYS I 103 18.880 117.610 88.097 1.00241.70 S ATOM 29211 SG CYS I 106 17.624 118.681 91.535 1.00237.36 S ATOM 29313 SG CYS J 7 62.839 90.495 37.800 1.00102.12 S ATOM 29336 SG CYS J 10 62.346 88.289 34.657 1.00115.67 S ATOM 29616 SG CYS J 45 59.378 89.174 36.926 1.00113.58 S ATOM 29622 SG CYS J 46 61.012 91.608 34.540 1.00116.12 S ATOM 30745 SG CYS L 31 96.214 113.809 53.895 1.00217.54 S ATOM 30765 SG CYS L 34 97.144 115.470 50.627 1.00214.51 S ATOM 30869 SG CYS L 48 99.791 114.542 53.201 1.00224.85 S ATOM 30892 SG CYS L 51 97.583 117.484 53.866 1.00230.28 S Time building chain proxies: 5.37, per 1000 atoms: 0.16 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: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " 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 B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " 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 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " 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 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " 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: 141 helices and 48 sheets defined 38.9% alpha, 20.0% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.648A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.706A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.582A 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: 3.911A 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 524 through 536 removed outlier: 3.681A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.567A 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 661 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 removed outlier: 3.558A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) 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 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.843A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 845 removed outlier: 3.930A 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 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.627A 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 Processing helix chain 'A' and resid 982 through 994 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 1057 removed outlier: 3.699A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1082 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1083 through 1087 removed outlier: 3.719A pdb=" N ALA A1087 " --> pdb=" O PHE A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.621A 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 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.928A 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 removed outlier: 3.516A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.678A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) 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: 3.942A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 removed outlier: 3.637A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.581A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.248A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.494A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (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: 3.621A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.739A 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 337 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.545A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) 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 439 removed outlier: 3.532A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.801A 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: 3.690A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.698A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.648A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 756 removed outlier: 3.656A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 756 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.601A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.063A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.645A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.771A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.262A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.857A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.600A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.560A 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 removed outlier: 3.563A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.168A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.528A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.515A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.564A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (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: 3.506A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix 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: 3.640A 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 21 through 35 removed outlier: 3.541A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) 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 65 removed outlier: 4.023A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.901A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (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 39 through 53 removed outlier: 3.699A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (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 90 removed outlier: 3.576A pdb=" N VAL A 241 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 86 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.817A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) 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 345 removed outlier: 3.616A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.763A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.826A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.912A 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: 3.506A 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 588 through 590 removed outlier: 7.046A 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 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 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1227 removed outlier: 4.343A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.125A 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: 4.709A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.483A 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: 4.709A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.791A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.791A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.540A 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 removed outlier: 6.107A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.003A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.151A 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: 4.197A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 641 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.554A 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: 5.216A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.918A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.565A 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: 6.918A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.189A 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: 7.172A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.092A 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: 3.512A pdb=" N ILE B 911 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 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 7 through 13 removed outlier: 6.776A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.794A 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: 6.591A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.409A 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: 6.409A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (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: 4.995A 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: 6.372A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 156 removed outlier: 3.781A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 86 through 94 removed outlier: 6.740A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.554A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.762A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.247A 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 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.991A 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 removed outlier: 6.582A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1364 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 8.51 Time building geometry restraints manager: 2.98 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: 5410 1.31 - 1.43: 8966 1.43 - 1.56: 19009 1.56 - 1.69: 196 1.69 - 1.81: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.181 0.193 1.00e-02 1.00e+04 3.71e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.208 0.162 1.20e-02 6.94e+03 1.81e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.445 -0.108 1.10e-02 8.26e+03 9.66e+01 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.330 0.079 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C2' ATP A1801 " pdb=" C3' ATP A1801 " ideal model delta sigma weight residual 1.531 1.453 0.078 1.20e-02 6.94e+03 4.19e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 46035 4.16 - 8.31: 114 8.31 - 12.47: 1 12.47 - 16.63: 2 16.63 - 20.78: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.45 -13.73 1.00e+00 1.00e+00 1.88e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 123.85 12.98 1.00e+00 1.00e+00 1.69e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.18 8.51 1.00e+00 1.00e+00 7.25e+01 angle pdb=" N3 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 127.04 133.30 -6.26 1.15e+00 7.59e-01 2.97e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.45: 19809 32.45 - 64.90: 615 64.90 - 97.34: 40 97.34 - 129.79: 1 129.79 - 162.24: 2 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 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+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 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+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 22.24 -162.24 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3319 0.033 - 0.065: 1234 0.065 - 0.098: 373 0.098 - 0.130: 242 0.130 - 0.163: 22 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.63e-01 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 6.39e-01 chirality pdb=" CB VAL B 482 " pdb=" CA VAL B 482 " pdb=" CG1 VAL B 482 " pdb=" CG2 VAL B 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C LEU A 710 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A1099 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A R 1 " 0.022 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A R 1 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A R 1 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A R 1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A R 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A R 1 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A R 1 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A R 1 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A R 1 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A R 1 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A R 1 " -0.003 2.00e-02 2.50e+03 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 76 2.38 - 3.01: 18057 3.01 - 3.64: 49121 3.64 - 4.27: 76107 4.27 - 4.90: 128233 Nonbonded interactions: 271594 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.752 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.843 2.170 nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.868 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1802 " model vdw 2.054 2.170 nonbonded pdb=" OG1 THR A 675 " pdb=" ND2 ASN A 736 " model vdw 2.082 3.120 ... (remaining 271589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 33.160 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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= 0.310 Angle : 0.607 20.781 46198 Z= 0.413 Chirality : 0.043 0.163 5190 Planarity : 0.003 0.044 5630 Dihedral : 14.435 162.241 13127 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.53 (0.14), residues: 3854 helix: 1.59 (0.15), residues: 1323 sheet: 0.03 (0.22), residues: 600 loop : -0.36 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1366 TYR 0.029 0.001 TYR B 797 PHE 0.015 0.001 PHE A 219 TRP 0.022 0.001 TRP A1044 HIS 0.011 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.31 (33873) covalent geometry : angle 0.60181 / 0.41 (46153) hydrogen bonds : bond 0.18377 / 12.09 ( 1428) hydrogen bonds : angle 6.80384 / 4.87 ( 3970) metal coordination : bond 0.00411 / 0.25 ( 32) metal coordination : angle 2.56541 / 1.59 ( 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 666 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.8649 (t-90) cc_final: 0.8376 (t-90) REVERT: A 123 ARG cc_start: 0.7337 (mtt90) cc_final: 0.7095 (mtm-85) REVERT: A 180 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7899 (mttp) REVERT: A 256 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6581 (mt0) REVERT: A 260 ASP cc_start: 0.8197 (t70) cc_final: 0.7909 (t0) REVERT: A 277 GLU cc_start: 0.8665 (tt0) cc_final: 0.7835 (tm-30) REVERT: A 281 HIS cc_start: 0.8135 (t70) cc_final: 0.7920 (t-90) REVERT: A 293 GLU cc_start: 0.8892 (tt0) cc_final: 0.8658 (tm-30) REVERT: A 317 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7598 (tmtt) REVERT: A 320 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7941 (mtm110) REVERT: A 330 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7826 (pttm) REVERT: A 332 LYS cc_start: 0.8701 (tttm) cc_final: 0.8224 (tptp) REVERT: A 333 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8712 (mm-30) REVERT: A 494 SER cc_start: 0.8610 (m) cc_final: 0.8252 (p) REVERT: A 542 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8107 (tp30) REVERT: A 618 GLU cc_start: 0.8334 (pm20) cc_final: 0.7957 (pm20) REVERT: A 636 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8248 (mm-30) REVERT: A 698 GLN cc_start: 0.7579 (tt0) cc_final: 0.7255 (tt0) REVERT: A 771 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8133 (mm-30) REVERT: A 780 VAL cc_start: 0.9001 (t) cc_final: 0.8637 (p) REVERT: A 903 ASN cc_start: 0.8223 (m110) cc_final: 0.7850 (m110) REVERT: A 961 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8100 (ttp80) REVERT: A 969 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8297 (mp10) REVERT: A 977 LYS cc_start: 0.9144 (tttp) cc_final: 0.8861 (mmmt) REVERT: A 1063 MET cc_start: 0.9129 (mmm) cc_final: 0.8929 (mmt) REVERT: A 1199 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7261 (tpp80) REVERT: A 1225 PHE cc_start: 0.7056 (t80) cc_final: 0.6740 (t80) REVERT: A 1265 ASN cc_start: 0.8151 (t0) cc_final: 0.7799 (m-40) REVERT: A 1280 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8691 (mt-10) REVERT: A 1315 GLU cc_start: 0.8758 (tt0) cc_final: 0.8369 (mt-10) REVERT: A 1336 MET cc_start: 0.8819 (ttt) cc_final: 0.8558 (ttp) REVERT: A 1350 LYS cc_start: 0.8012 (tttm) cc_final: 0.7797 (ttmm) REVERT: A 1411 GLU cc_start: 0.8462 (tp30) cc_final: 0.7651 (tp30) REVERT: A 1433 MET cc_start: 0.9238 (ttp) cc_final: 0.8987 (ttp) REVERT: B 21 GLU cc_start: 0.8770 (pt0) cc_final: 0.8314 (pm20) REVERT: B 101 MET cc_start: 0.9039 (mtt) cc_final: 0.8814 (mtp) REVERT: B 103 ASN cc_start: 0.8637 (p0) cc_final: 0.8426 (p0) REVERT: B 133 LYS cc_start: 0.8494 (mttt) cc_final: 0.8132 (tppp) REVERT: B 272 THR cc_start: 0.9080 (m) cc_final: 0.8634 (p) REVERT: B 304 ASP cc_start: 0.8176 (t70) cc_final: 0.7818 (t0) REVERT: B 319 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7862 (tm-30) REVERT: B 358 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8009 (mmtt) REVERT: B 399 ASP cc_start: 0.9143 (m-30) cc_final: 0.8899 (m-30) REVERT: B 433 GLN cc_start: 0.7594 (pt0) cc_final: 0.7343 (tm-30) REVERT: B 471 LYS cc_start: 0.8031 (mptt) cc_final: 0.7819 (mttt) REVERT: B 508 LEU cc_start: 0.8300 (mm) cc_final: 0.8073 (mp) REVERT: B 531 GLN cc_start: 0.8424 (pm20) cc_final: 0.7905 (tm-30) REVERT: B 595 ARG cc_start: 0.8571 (ttt180) cc_final: 0.7919 (ttp-110) REVERT: B 619 ILE cc_start: 0.8965 (mm) cc_final: 0.8760 (mm) REVERT: B 622 LYS cc_start: 0.8177 (mttt) cc_final: 0.7944 (mtmm) REVERT: B 629 ASP cc_start: 0.8347 (t0) cc_final: 0.8062 (p0) REVERT: B 641 GLU cc_start: 0.8408 (tt0) cc_final: 0.8148 (pp20) REVERT: B 666 TYR cc_start: 0.8094 (t80) cc_final: 0.7776 (m-10) REVERT: B 885 MET cc_start: 0.6196 (mmm) cc_final: 0.5489 (mmm) REVERT: B 936 ASP cc_start: 0.7456 (p0) cc_final: 0.7240 (t0) REVERT: B 1049 ASP cc_start: 0.8943 (m-30) cc_final: 0.8679 (p0) REVERT: C 19 ASP cc_start: 0.8378 (t0) cc_final: 0.8166 (t0) REVERT: C 94 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7870 (ttmm) REVERT: C 125 MET cc_start: 0.8858 (mtp) cc_final: 0.8631 (mtm) REVERT: C 136 ASP cc_start: 0.7466 (t70) cc_final: 0.7120 (t0) REVERT: C 209 TYR cc_start: 0.9166 (m-80) cc_final: 0.8652 (m-80) REVERT: D 198 LEU cc_start: 0.6066 (mt) cc_final: 0.5777 (tp) REVERT: D 219 THR cc_start: 0.4860 (t) cc_final: 0.4526 (p) REVERT: E 6 GLU cc_start: 0.8529 (tp30) cc_final: 0.8045 (tp30) REVERT: E 7 ARG cc_start: 0.8275 (ttt180) cc_final: 0.8051 (mtm-85) REVERT: E 8 ASN cc_start: 0.8912 (m-40) cc_final: 0.8701 (m-40) REVERT: E 106 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8104 (mm110) REVERT: F 76 LYS cc_start: 0.9114 (tptt) cc_final: 0.8827 (tppp) REVERT: F 78 GLN cc_start: 0.8921 (mt0) cc_final: 0.8635 (mt0) REVERT: F 104 ASN cc_start: 0.8847 (m-40) cc_final: 0.8554 (t0) REVERT: F 114 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8266 (mm-30) REVERT: F 119 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8238 (mmm-85) REVERT: F 123 LYS cc_start: 0.8696 (tttm) cc_final: 0.8457 (ttmt) REVERT: F 144 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8510 (mt-10) REVERT: G 28 THR cc_start: 0.8311 (m) cc_final: 0.8071 (p) REVERT: G 41 LYS cc_start: 0.7900 (tppt) cc_final: 0.7699 (ttpt) REVERT: G 50 ASP cc_start: 0.7518 (t0) cc_final: 0.7316 (t0) REVERT: G 73 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7785 (mtpp) REVERT: G 106 MET cc_start: 0.5527 (ttp) cc_final: 0.5312 (ptm) REVERT: G 140 LYS cc_start: 0.5916 (mttt) cc_final: 0.5578 (tptm) REVERT: H 8 ASP cc_start: 0.8808 (t0) cc_final: 0.8297 (t0) REVERT: H 27 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7929 (mp0) REVERT: H 32 THR cc_start: 0.9027 (m) cc_final: 0.8766 (p) REVERT: H 33 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7111 (tp40) REVERT: H 103 LYS cc_start: 0.8747 (tptt) cc_final: 0.8483 (tppt) REVERT: J 1 MET cc_start: 0.8241 (mtm) cc_final: 0.7977 (mtt) REVERT: J 26 GLN cc_start: 0.8255 (tt0) cc_final: 0.7829 (tm-30) REVERT: J 42 LYS cc_start: 0.8955 (pttt) cc_final: 0.8559 (pttp) REVERT: J 49 MET cc_start: 0.9305 (tpp) cc_final: 0.8812 (tpp) REVERT: K 17 SER cc_start: 0.8900 (m) cc_final: 0.8466 (p) REVERT: K 20 LYS cc_start: 0.8650 (tttp) cc_final: 0.8356 (ttpp) REVERT: K 26 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8516 (mtmm) REVERT: K 36 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8422 (mm-30) REVERT: K 38 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7999 (mm-30) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.2447 time to fit residues: 250.0276 Evaluate side-chains 415 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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: 40.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN A1432 GLN B 110 HIS B 178 ASN B 325 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN D 34 GLN D 37 GLN D 41 GLN E 113 GLN G 122 ASN H 137 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.087228 restraints weight = 50823.766| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.10 r_work: 0.2992 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 33905 Z= 0.307 Angle : 0.660 8.351 46198 Z= 0.351 Chirality : 0.048 0.264 5190 Planarity : 0.005 0.043 5630 Dihedral : 16.570 161.033 5346 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 1.22 % Allowed : 6.00 % Favored : 92.78 % 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: 0.32 (0.14), residues: 3854 helix: 1.34 (0.14), residues: 1342 sheet: -0.06 (0.21), residues: 630 loop : -0.46 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 287 TYR 0.021 0.002 TYR B 797 PHE 0.023 0.002 PHE A 219 TRP 0.018 0.002 TRP A1044 HIS 0.011 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.31 (33873) covalent geometry : angle 0.65204 / 0.35 (46153) hydrogen bonds : bond 0.05298 / 3.51 ( 1428) hydrogen bonds : angle 5.22815 / 3.71 ( 3970) metal coordination : bond 0.01141 / 0.74 ( 32) metal coordination : angle 3.40707 / 2.11 ( 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 460 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 418 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9027 (mttm) cc_final: 0.8750 (mtmt) REVERT: A 180 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8420 (mttp) REVERT: A 259 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8254 (mm-30) REVERT: A 277 GLU cc_start: 0.8710 (tt0) cc_final: 0.8039 (tm-30) REVERT: A 317 LYS cc_start: 0.8678 (mmtt) cc_final: 0.7951 (tmtt) REVERT: A 320 ARG cc_start: 0.8285 (mtm110) cc_final: 0.8082 (mtm110) REVERT: A 330 LYS cc_start: 0.8898 (ptmt) cc_final: 0.8508 (pttm) REVERT: A 618 GLU cc_start: 0.8496 (pm20) cc_final: 0.8287 (pm20) REVERT: A 676 MET cc_start: 0.9194 (mmm) cc_final: 0.8968 (mmt) REVERT: A 698 GLN cc_start: 0.8173 (tt0) cc_final: 0.7965 (tt0) REVERT: A 780 VAL cc_start: 0.9458 (t) cc_final: 0.9118 (p) REVERT: A 902 LEU cc_start: 0.8046 (mt) cc_final: 0.7692 (mt) REVERT: A 903 ASN cc_start: 0.8443 (m110) cc_final: 0.8043 (m110) REVERT: A 1209 MET cc_start: 0.7614 (mmt) cc_final: 0.7291 (mmm) REVERT: A 1217 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7655 (mmtm) REVERT: A 1225 PHE cc_start: 0.7714 (t80) cc_final: 0.7486 (t80) REVERT: A 1259 MET cc_start: 0.7559 (mtm) cc_final: 0.7259 (mtm) REVERT: A 1265 ASN cc_start: 0.8242 (t0) cc_final: 0.7949 (m-40) REVERT: A 1270 ASN cc_start: 0.8842 (m-40) cc_final: 0.8618 (m-40) REVERT: A 1411 GLU cc_start: 0.8716 (tp30) cc_final: 0.8150 (tp30) REVERT: A 1433 MET cc_start: 0.9313 (ttp) cc_final: 0.9082 (ttp) REVERT: B 72 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: B 133 LYS cc_start: 0.8840 (mttt) cc_final: 0.8639 (tppp) REVERT: B 135 ARG cc_start: 0.7932 (mpp80) cc_final: 0.7716 (mpp80) REVERT: B 272 THR cc_start: 0.9382 (m) cc_final: 0.8987 (p) REVERT: B 304 ASP cc_start: 0.8583 (t70) cc_final: 0.8215 (t0) REVERT: B 358 LYS cc_start: 0.8649 (mmtm) cc_final: 0.8358 (mptt) REVERT: B 391 ASP cc_start: 0.8563 (m-30) cc_final: 0.8190 (m-30) REVERT: B 508 LEU cc_start: 0.8564 (mm) cc_final: 0.8282 (mp) REVERT: B 595 ARG cc_start: 0.8974 (ttt180) cc_final: 0.8484 (ttp-110) REVERT: B 619 ILE cc_start: 0.9178 (mm) cc_final: 0.8971 (mt) REVERT: B 622 LYS cc_start: 0.8973 (mttt) cc_final: 0.8759 (mtmm) REVERT: B 885 MET cc_start: 0.7063 (mmm) cc_final: 0.6061 (mmm) REVERT: C 75 MET cc_start: 0.9091 (mmm) cc_final: 0.8455 (tpp) REVERT: C 94 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8269 (ttmm) REVERT: C 136 ASP cc_start: 0.7693 (t70) cc_final: 0.7492 (t0) REVERT: D 1 MET cc_start: 0.2298 (tmm) cc_final: 0.0106 (ttp) REVERT: D 66 ARG cc_start: 0.6546 (ttm170) cc_final: 0.6311 (mtp180) REVERT: E 3 GLN cc_start: 0.7438 (mt0) cc_final: 0.7152 (pm20) REVERT: E 6 GLU cc_start: 0.8594 (tp30) cc_final: 0.8263 (tp30) REVERT: E 84 ASP cc_start: 0.8983 (t70) cc_final: 0.8729 (t0) REVERT: F 76 LYS cc_start: 0.9400 (tptt) cc_final: 0.9185 (tppt) REVERT: G 50 ASP cc_start: 0.8000 (t0) cc_final: 0.7601 (t0) REVERT: G 75 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7723 (mmm-85) REVERT: G 140 LYS cc_start: 0.6159 (mttt) cc_final: 0.5797 (tptm) REVERT: H 32 THR cc_start: 0.9090 (m) cc_final: 0.8875 (p) REVERT: H 33 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7643 (tp40) REVERT: H 52 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7930 (mm110) REVERT: J 26 GLN cc_start: 0.8422 (tt0) cc_final: 0.8193 (mt0) REVERT: K 5 ASP cc_start: 0.8785 (m-30) cc_final: 0.8416 (m-30) REVERT: K 8 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8326 (mt-10) REVERT: K 17 SER cc_start: 0.9244 (m) cc_final: 0.8924 (t) REVERT: L 68 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8419 (tt0) outliers start: 42 outliers final: 32 residues processed: 438 average time/residue: 0.2344 time to fit residues: 161.6460 Evaluate side-chains 400 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 367 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1147 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 333 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 249 optimal weight: 0.6980 chunk 222 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN A 975 HIS A 996 ASN B 178 ASN G 57 GLN G 71 ASN H 52 GLN H 137 GLN I 90 GLN K 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089466 restraints weight = 50342.928| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.17 r_work: 0.2999 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1850 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= 0.127 Angle : 0.546 7.803 46198 Z= 0.292 Chirality : 0.044 0.264 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.441 159.061 5346 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 1.02 % Allowed : 8.04 % Favored : 90.94 % 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: 1.47 (0.15), residues: 1344 sheet: 0.00 (0.21), residues: 614 loop : -0.41 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 91 TYR 0.017 0.001 TYR I 44 PHE 0.019 0.001 PHE A 219 TRP 0.016 0.001 TRP A1044 HIS 0.010 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (33873) covalent geometry : angle 0.53927 / 0.29 (46153) hydrogen bonds : bond 0.03994 / 2.67 ( 1428) hydrogen bonds : angle 4.72803 / 3.34 ( 3970) metal coordination : bond 0.00482 / 0.29 ( 32) metal coordination : angle 2.87622 / 1.81 ( 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 435 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 400 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9027 (mttm) cc_final: 0.8741 (mtmt) REVERT: A 277 GLU cc_start: 0.8725 (tt0) cc_final: 0.8038 (tm-30) REVERT: A 330 LYS cc_start: 0.8761 (ptmt) cc_final: 0.8358 (pttp) REVERT: A 618 GLU cc_start: 0.8498 (pm20) cc_final: 0.8255 (pm20) REVERT: A 698 GLN cc_start: 0.8229 (tt0) cc_final: 0.7969 (tt0) REVERT: A 902 LEU cc_start: 0.8108 (mt) cc_final: 0.7771 (mt) REVERT: A 903 ASN cc_start: 0.8439 (m110) cc_final: 0.8037 (m110) REVERT: A 1209 MET cc_start: 0.7595 (mmt) cc_final: 0.7244 (mmm) REVERT: A 1217 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7569 (mmtm) REVERT: A 1225 PHE cc_start: 0.7716 (t80) cc_final: 0.7426 (t80) REVERT: A 1259 MET cc_start: 0.7518 (mtm) cc_final: 0.7214 (mtm) REVERT: A 1265 ASN cc_start: 0.8204 (t0) cc_final: 0.7929 (m-40) REVERT: A 1411 GLU cc_start: 0.8683 (tp30) cc_final: 0.8093 (tp30) REVERT: B 72 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: B 133 LYS cc_start: 0.8848 (mttt) cc_final: 0.8580 (ttmm) REVERT: B 272 THR cc_start: 0.9325 (m) cc_final: 0.8903 (p) REVERT: B 304 ASP cc_start: 0.8455 (t70) cc_final: 0.8183 (t0) REVERT: B 358 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8415 (mmtt) REVERT: B 370 PHE cc_start: 0.8557 (m-10) cc_final: 0.8300 (m-10) REVERT: B 470 LYS cc_start: 0.9089 (mppt) cc_final: 0.8765 (ptmt) REVERT: B 508 LEU cc_start: 0.8544 (mm) cc_final: 0.8255 (mp) REVERT: B 595 ARG cc_start: 0.8886 (ttt180) cc_final: 0.8409 (ttp-110) REVERT: B 622 LYS cc_start: 0.8912 (mttt) cc_final: 0.8670 (mtmm) REVERT: B 885 MET cc_start: 0.6527 (mmm) cc_final: 0.6075 (mmm) REVERT: C 75 MET cc_start: 0.9053 (mmm) cc_final: 0.8415 (tpp) REVERT: C 94 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8257 (ttmm) REVERT: C 136 ASP cc_start: 0.7613 (t70) cc_final: 0.7383 (t0) REVERT: D 54 GLU cc_start: 0.8031 (tt0) cc_final: 0.7759 (pt0) REVERT: D 66 ARG cc_start: 0.6545 (ttm170) cc_final: 0.6327 (mtp180) REVERT: E 3 GLN cc_start: 0.7131 (mt0) cc_final: 0.6794 (pm20) REVERT: E 6 GLU cc_start: 0.8568 (tp30) cc_final: 0.8182 (tp30) REVERT: F 76 LYS cc_start: 0.9315 (tptt) cc_final: 0.9003 (tppp) REVERT: G 50 ASP cc_start: 0.7923 (t0) cc_final: 0.7469 (t0) REVERT: G 75 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7811 (mmm-85) REVERT: G 140 LYS cc_start: 0.6089 (mttt) cc_final: 0.5739 (tptm) REVERT: H 33 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7530 (tp40) REVERT: H 52 GLN cc_start: 0.8503 (mm110) cc_final: 0.8163 (mm-40) REVERT: H 91 ASP cc_start: 0.8742 (m-30) cc_final: 0.8467 (m-30) REVERT: I 97 MET cc_start: 0.8271 (mtp) cc_final: 0.8048 (mtt) REVERT: J 26 GLN cc_start: 0.8339 (tt0) cc_final: 0.8108 (mt0) REVERT: L 68 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8423 (tt0) outliers start: 35 outliers final: 25 residues processed: 415 average time/residue: 0.2051 time to fit residues: 136.2198 Evaluate side-chains 380 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 354 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS D 137 ASN D 150 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 71 ASN H 137 GLN I 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.084591 restraints weight = 50758.398| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.07 r_work: 0.2947 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 33905 Z= 0.364 Angle : 0.709 10.902 46198 Z= 0.368 Chirality : 0.049 0.278 5190 Planarity : 0.005 0.051 5630 Dihedral : 16.574 161.062 5346 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 2.18 % Allowed : 9.55 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 3854 helix: 1.14 (0.14), residues: 1331 sheet: -0.25 (0.20), residues: 632 loop : -0.63 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 335 TYR 0.024 0.002 TYR E 187 PHE 0.029 0.002 PHE A 219 TRP 0.020 0.002 TRP A1228 HIS 0.012 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00877 / 0.36 (33873) covalent geometry : angle 0.69735 / 0.37 (46153) hydrogen bonds : bond 0.04802 / 3.19 ( 1428) hydrogen bonds : angle 4.87243 / 3.45 ( 3970) metal coordination : bond 0.01452 / 0.97 ( 32) metal coordination : angle 4.12463 / 2.57 ( 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 431 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 356 time to evaluate : 1.232 Fit side-chains REVERT: A 123 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7562 (mtm-85) REVERT: A 133 LYS cc_start: 0.9065 (mttm) cc_final: 0.8789 (mtmt) REVERT: A 277 GLU cc_start: 0.8705 (tt0) cc_final: 0.8059 (tm-30) REVERT: A 293 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8458 (tm-30) REVERT: A 330 LYS cc_start: 0.8914 (ptmt) cc_final: 0.8489 (pttm) REVERT: A 470 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8811 (pp) REVERT: A 698 GLN cc_start: 0.8357 (tt0) cc_final: 0.8064 (tt0) REVERT: A 780 VAL cc_start: 0.9471 (t) cc_final: 0.9165 (p) REVERT: A 1209 MET cc_start: 0.7216 (mmt) cc_final: 0.7011 (mmm) REVERT: A 1217 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7628 (mmtm) REVERT: A 1225 PHE cc_start: 0.7820 (t80) cc_final: 0.7565 (t80) REVERT: A 1228 TRP cc_start: 0.8184 (p90) cc_final: 0.7925 (p90) REVERT: A 1259 MET cc_start: 0.7487 (mtm) cc_final: 0.7164 (mtm) REVERT: A 1265 ASN cc_start: 0.8222 (t0) cc_final: 0.7822 (m-40) REVERT: A 1411 GLU cc_start: 0.8716 (tp30) cc_final: 0.8138 (tp30) REVERT: B 72 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: B 272 THR cc_start: 0.9352 (m) cc_final: 0.8915 (p) REVERT: B 304 ASP cc_start: 0.8553 (t70) cc_final: 0.8171 (t0) REVERT: B 470 LYS cc_start: 0.9129 (mppt) cc_final: 0.8832 (ptmt) REVERT: B 595 ARG cc_start: 0.9068 (ttt180) cc_final: 0.8480 (ttp-110) REVERT: B 598 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 618 ASP cc_start: 0.9033 (t0) cc_final: 0.8781 (t0) REVERT: B 622 LYS cc_start: 0.9006 (mttt) cc_final: 0.8733 (mtmm) REVERT: C 75 MET cc_start: 0.9087 (mmm) cc_final: 0.8568 (tpp) REVERT: C 94 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8183 (ttmm) REVERT: C 136 ASP cc_start: 0.7708 (t70) cc_final: 0.7472 (t0) REVERT: D 54 GLU cc_start: 0.8010 (tt0) cc_final: 0.7740 (pt0) REVERT: D 66 ARG cc_start: 0.6693 (ttm170) cc_final: 0.6458 (mtp180) REVERT: E 6 GLU cc_start: 0.8762 (tp30) cc_final: 0.8335 (tp30) REVERT: E 50 MET cc_start: 0.8327 (ppp) cc_final: 0.8005 (ppp) REVERT: F 76 LYS cc_start: 0.9354 (tptt) cc_final: 0.9086 (tppp) REVERT: G 1 MET cc_start: 0.7172 (tpp) cc_final: 0.6351 (tmm) REVERT: G 44 TYR cc_start: 0.7037 (m-80) cc_final: 0.6810 (m-80) REVERT: G 50 ASP cc_start: 0.7988 (t0) cc_final: 0.7596 (t0) REVERT: G 53 ASN cc_start: 0.8997 (t0) cc_final: 0.8704 (t0) REVERT: G 75 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7814 (mmm-85) REVERT: G 140 LYS cc_start: 0.6335 (mttt) cc_final: 0.5950 (tptm) REVERT: H 33 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7661 (tp40) REVERT: H 91 ASP cc_start: 0.8753 (m-30) cc_final: 0.8501 (m-30) REVERT: J 26 GLN cc_start: 0.8421 (tt0) cc_final: 0.8185 (mt0) REVERT: K 5 ASP cc_start: 0.8744 (m-30) cc_final: 0.8393 (m-30) REVERT: L 68 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8498 (tt0) outliers start: 75 outliers final: 52 residues processed: 397 average time/residue: 0.2445 time to fit residues: 154.1067 Evaluate side-chains 387 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 333 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 GLN A 975 HIS B 325 GLN D 2 ASN D 146 GLN G 24 GLN I 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088751 restraints weight = 50177.959| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.15 r_work: 0.2981 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33905 Z= 0.122 Angle : 0.539 8.843 46198 Z= 0.285 Chirality : 0.043 0.269 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.463 159.365 5346 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 1.51 % Allowed : 11.36 % Favored : 87.13 % 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: 0.32 (0.14), residues: 3854 helix: 1.44 (0.14), residues: 1344 sheet: -0.11 (0.21), residues: 613 loop : -0.53 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.017 0.001 TYR E 187 PHE 0.017 0.001 PHE A 219 TRP 0.016 0.001 TRP A1044 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (33873) covalent geometry : angle 0.53103 / 0.28 (46153) hydrogen bonds : bond 0.03650 / 2.45 ( 1428) hydrogen bonds : angle 4.48042 / 3.16 ( 3970) metal coordination : bond 0.00522 / 0.32 ( 32) metal coordination : angle 3.02508 / 1.92 ( 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 424 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 372 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7337 (mtm-85) REVERT: A 133 LYS cc_start: 0.9068 (mttm) cc_final: 0.8751 (mtmt) REVERT: A 277 GLU cc_start: 0.8741 (tt0) cc_final: 0.8058 (tm-30) REVERT: A 330 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8325 (pttm) REVERT: A 470 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8653 (pp) REVERT: A 542 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 1209 MET cc_start: 0.7178 (mmt) cc_final: 0.6956 (mmm) REVERT: A 1217 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7545 (mmtm) REVERT: A 1225 PHE cc_start: 0.7679 (t80) cc_final: 0.7370 (t80) REVERT: A 1228 TRP cc_start: 0.8225 (p90) cc_final: 0.7786 (p90) REVERT: A 1259 MET cc_start: 0.7570 (mtm) cc_final: 0.7245 (mtm) REVERT: A 1265 ASN cc_start: 0.8259 (t0) cc_final: 0.7862 (m-40) REVERT: A 1411 GLU cc_start: 0.8657 (tp30) cc_final: 0.8076 (tp30) REVERT: B 72 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: B 133 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7993 (tppt) REVERT: B 272 THR cc_start: 0.9281 (m) cc_final: 0.8846 (p) REVERT: B 304 ASP cc_start: 0.8503 (t70) cc_final: 0.8204 (t0) REVERT: B 370 PHE cc_start: 0.8576 (m-10) cc_final: 0.8275 (m-10) REVERT: B 470 LYS cc_start: 0.9132 (mppt) cc_final: 0.8799 (ptmt) REVERT: B 595 ARG cc_start: 0.8935 (ttt180) cc_final: 0.8304 (ttp-110) REVERT: B 598 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 618 ASP cc_start: 0.8952 (t0) cc_final: 0.8705 (t0) REVERT: B 622 LYS cc_start: 0.8934 (mttt) cc_final: 0.8659 (mtmm) REVERT: B 628 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9372 (p) REVERT: C 75 MET cc_start: 0.9035 (mmm) cc_final: 0.8381 (tpp) REVERT: C 94 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8126 (ttmm) REVERT: C 136 ASP cc_start: 0.7648 (t70) cc_final: 0.7372 (t0) REVERT: D 1 MET cc_start: 0.1039 (tmm) cc_final: -0.0822 (ttp) REVERT: D 54 GLU cc_start: 0.7982 (tt0) cc_final: 0.7700 (pt0) REVERT: D 66 ARG cc_start: 0.6633 (ttm170) cc_final: 0.6403 (mtp180) REVERT: E 3 GLN cc_start: 0.7483 (tt0) cc_final: 0.7128 (tm-30) REVERT: E 6 GLU cc_start: 0.8698 (tp30) cc_final: 0.8309 (tp30) REVERT: E 50 MET cc_start: 0.8468 (ppp) cc_final: 0.7694 (ppp) REVERT: F 76 LYS cc_start: 0.9346 (tptt) cc_final: 0.9074 (tppp) REVERT: G 1 MET cc_start: 0.7014 (tpp) cc_final: 0.6242 (tmm) REVERT: G 50 ASP cc_start: 0.7858 (t0) cc_final: 0.7484 (t0) REVERT: G 53 ASN cc_start: 0.9084 (t0) cc_final: 0.8791 (t0) REVERT: G 75 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7799 (mmm-85) REVERT: G 140 LYS cc_start: 0.6272 (mttt) cc_final: 0.5874 (tptm) REVERT: H 33 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7551 (tp40) REVERT: J 26 GLN cc_start: 0.8388 (tt0) cc_final: 0.8146 (mt0) REVERT: K 5 ASP cc_start: 0.8683 (m-30) cc_final: 0.8106 (m-30) REVERT: K 54 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8569 (mmm160) REVERT: L 68 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8426 (tt0) outliers start: 52 outliers final: 33 residues processed: 402 average time/residue: 0.2164 time to fit residues: 138.3472 Evaluate side-chains 378 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 chunk 143 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 293 optimal weight: 0.1980 overall best weight: 2.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 HIS D 146 GLN G 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086677 restraints weight = 50356.829| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.14 r_work: 0.2967 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33905 Z= 0.212 Angle : 0.573 11.102 46198 Z= 0.300 Chirality : 0.044 0.270 5190 Planarity : 0.004 0.044 5630 Dihedral : 16.460 159.531 5346 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.78 % Allowed : 12.03 % Favored : 86.20 % 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: 0.30 (0.14), residues: 3854 helix: 1.42 (0.14), residues: 1344 sheet: -0.09 (0.21), residues: 610 loop : -0.55 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.020 0.001 TYR E 187 PHE 0.024 0.001 PHE A 219 TRP 0.014 0.001 TRP A1044 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (33873) covalent geometry : angle 0.56403 / 0.30 (46153) hydrogen bonds : bond 0.03845 / 2.56 ( 1428) hydrogen bonds : angle 4.48339 / 3.17 ( 3970) metal coordination : bond 0.00901 / 0.59 ( 32) metal coordination : angle 3.25946 / 2.05 ( 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 411 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 350 time to evaluate : 1.305 Fit side-chains REVERT: A 61 ILE cc_start: 0.8544 (pt) cc_final: 0.8157 (mt) REVERT: A 123 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7296 (mtm-85) REVERT: A 133 LYS cc_start: 0.9062 (mttm) cc_final: 0.8766 (mtmt) REVERT: A 277 GLU cc_start: 0.8754 (tt0) cc_final: 0.8096 (tm-30) REVERT: A 293 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8415 (tm-30) REVERT: A 330 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8390 (pttm) REVERT: A 470 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8732 (pp) REVERT: A 1209 MET cc_start: 0.7308 (mmt) cc_final: 0.7074 (mmm) REVERT: A 1217 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7486 (mmtm) REVERT: A 1225 PHE cc_start: 0.7698 (t80) cc_final: 0.7421 (t80) REVERT: A 1228 TRP cc_start: 0.8288 (p90) cc_final: 0.7811 (p90) REVERT: A 1259 MET cc_start: 0.7373 (mtm) cc_final: 0.7140 (mtm) REVERT: A 1265 ASN cc_start: 0.8247 (t0) cc_final: 0.7851 (m-40) REVERT: A 1411 GLU cc_start: 0.8695 (tp30) cc_final: 0.8120 (tp30) REVERT: B 72 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: B 272 THR cc_start: 0.9301 (m) cc_final: 0.8863 (p) REVERT: B 304 ASP cc_start: 0.8506 (t70) cc_final: 0.8192 (t0) REVERT: B 370 PHE cc_start: 0.8594 (m-10) cc_final: 0.8282 (m-10) REVERT: B 470 LYS cc_start: 0.9139 (mppt) cc_final: 0.8812 (ptmt) REVERT: B 595 ARG cc_start: 0.8999 (ttt180) cc_final: 0.8352 (ttp-110) REVERT: B 598 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 618 ASP cc_start: 0.8964 (t0) cc_final: 0.8733 (t0) REVERT: B 622 LYS cc_start: 0.8968 (mttt) cc_final: 0.8692 (mtmm) REVERT: B 628 THR cc_start: 0.9615 (OUTLIER) cc_final: 0.9397 (p) REVERT: B 1065 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: C 75 MET cc_start: 0.9067 (mmm) cc_final: 0.8503 (tpp) REVERT: C 94 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8131 (ttmm) REVERT: C 136 ASP cc_start: 0.7719 (t70) cc_final: 0.7436 (t0) REVERT: D 1 MET cc_start: 0.1061 (tmm) cc_final: -0.0909 (ttp) REVERT: D 66 ARG cc_start: 0.6643 (ttm170) cc_final: 0.6419 (mtp180) REVERT: E 6 GLU cc_start: 0.8779 (tp30) cc_final: 0.8377 (tp30) REVERT: E 50 MET cc_start: 0.8477 (ppp) cc_final: 0.8088 (ppp) REVERT: F 76 LYS cc_start: 0.9339 (tptt) cc_final: 0.9093 (tppp) REVERT: G 50 ASP cc_start: 0.7865 (t0) cc_final: 0.7498 (t0) REVERT: G 53 ASN cc_start: 0.9099 (t0) cc_final: 0.8799 (t0) REVERT: G 75 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7951 (mmm-85) REVERT: G 140 LYS cc_start: 0.6288 (mttt) cc_final: 0.5893 (tptm) REVERT: H 33 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7578 (tp40) REVERT: H 91 ASP cc_start: 0.8759 (m-30) cc_final: 0.8494 (m-30) REVERT: J 26 GLN cc_start: 0.8389 (tt0) cc_final: 0.8138 (mt0) REVERT: K 5 ASP cc_start: 0.8775 (m-30) cc_final: 0.8219 (m-30) REVERT: L 68 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8442 (tt0) outliers start: 61 outliers final: 48 residues processed: 385 average time/residue: 0.2120 time to fit residues: 129.4717 Evaluate side-chains 391 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 354 optimal weight: 0.0970 chunk 270 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 351 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.086986 restraints weight = 50475.881| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.14 r_work: 0.2974 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33905 Z= 0.192 Angle : 0.558 11.797 46198 Z= 0.292 Chirality : 0.044 0.268 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.463 159.001 5346 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 1.83 % Allowed : 12.46 % Favored : 85.70 % 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: 0.30 (0.14), residues: 3854 helix: 1.44 (0.14), residues: 1344 sheet: -0.11 (0.21), residues: 612 loop : -0.55 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.019 0.001 TYR E 187 PHE 0.022 0.001 PHE A 219 TRP 0.014 0.001 TRP A1044 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (33873) covalent geometry : angle 0.54912 / 0.29 (46153) hydrogen bonds : bond 0.03719 / 2.48 ( 1428) hydrogen bonds : angle 4.42991 / 3.13 ( 3970) metal coordination : bond 0.00817 / 0.53 ( 32) metal coordination : angle 3.17661 / 2.00 ( 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 409 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 133 LYS cc_start: 0.9075 (mttm) cc_final: 0.8795 (mtmt) REVERT: A 277 GLU cc_start: 0.8734 (tt0) cc_final: 0.8082 (tm-30) REVERT: A 293 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 330 LYS cc_start: 0.8778 (ptmt) cc_final: 0.8381 (pttm) REVERT: A 470 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8747 (pp) REVERT: A 1217 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7502 (mmtm) REVERT: A 1225 PHE cc_start: 0.7679 (t80) cc_final: 0.7359 (t80) REVERT: A 1228 TRP cc_start: 0.8310 (p90) cc_final: 0.7731 (p90) REVERT: A 1259 MET cc_start: 0.7414 (mtm) cc_final: 0.7180 (mtm) REVERT: A 1265 ASN cc_start: 0.8244 (t0) cc_final: 0.7843 (m-40) REVERT: A 1411 GLU cc_start: 0.8680 (tp30) cc_final: 0.8110 (tp30) REVERT: B 72 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: B 272 THR cc_start: 0.9296 (m) cc_final: 0.8854 (p) REVERT: B 304 ASP cc_start: 0.8503 (t70) cc_final: 0.8183 (t70) REVERT: B 370 PHE cc_start: 0.8570 (m-10) cc_final: 0.8259 (m-10) REVERT: B 470 LYS cc_start: 0.9128 (mppt) cc_final: 0.8811 (ptmt) REVERT: B 595 ARG cc_start: 0.9000 (ttt180) cc_final: 0.8596 (tmm160) REVERT: B 598 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8319 (tm-30) REVERT: B 618 ASP cc_start: 0.8963 (t0) cc_final: 0.8728 (t0) REVERT: B 622 LYS cc_start: 0.8975 (mttt) cc_final: 0.8701 (mtmm) REVERT: B 629 ASP cc_start: 0.8646 (t0) cc_final: 0.8419 (t0) REVERT: B 1065 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: C 75 MET cc_start: 0.9075 (mmm) cc_final: 0.8685 (tpp) REVERT: C 94 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8138 (ttmm) REVERT: C 136 ASP cc_start: 0.7721 (t70) cc_final: 0.7445 (t0) REVERT: D 1 MET cc_start: 0.1064 (tmm) cc_final: -0.0895 (ttp) REVERT: D 66 ARG cc_start: 0.6674 (ttm170) cc_final: 0.6411 (mtp180) REVERT: E 6 GLU cc_start: 0.8846 (tp30) cc_final: 0.8410 (tp30) REVERT: E 50 MET cc_start: 0.8502 (ppp) cc_final: 0.8097 (ppp) REVERT: F 76 LYS cc_start: 0.9336 (tptt) cc_final: 0.9090 (tppp) REVERT: F 114 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8153 (mm-30) REVERT: G 50 ASP cc_start: 0.7907 (t0) cc_final: 0.7554 (t0) REVERT: G 53 ASN cc_start: 0.9107 (t0) cc_final: 0.8801 (t0) REVERT: G 75 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7941 (mmm-85) REVERT: G 140 LYS cc_start: 0.6282 (mttt) cc_final: 0.5888 (tptm) REVERT: H 33 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7583 (tp40) REVERT: H 91 ASP cc_start: 0.8755 (m-30) cc_final: 0.8512 (m-30) REVERT: J 26 GLN cc_start: 0.8386 (tt0) cc_final: 0.8128 (mt0) REVERT: K 5 ASP cc_start: 0.8793 (m-30) cc_final: 0.8418 (m-30) REVERT: K 54 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8595 (mmm160) REVERT: L 68 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8437 (tt0) outliers start: 63 outliers final: 49 residues processed: 383 average time/residue: 0.2208 time to fit residues: 134.6190 Evaluate side-chains 391 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 338 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 331 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 126 optimal weight: 0.3980 chunk 275 optimal weight: 0.0070 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 HIS ** B 762 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 = 0.3781 r_free = 0.3781 target = 0.133948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089771 restraints weight = 50131.564| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.16 r_work: 0.3001 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33905 Z= 0.103 Angle : 0.512 11.950 46198 Z= 0.271 Chirality : 0.042 0.261 5190 Planarity : 0.003 0.046 5630 Dihedral : 16.371 157.681 5346 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 1.51 % Allowed : 12.87 % Favored : 85.61 % 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: 0.46 (0.14), residues: 3854 helix: 1.59 (0.14), residues: 1351 sheet: -0.02 (0.21), residues: 602 loop : -0.49 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 320 TYR 0.017 0.001 TYR E 187 PHE 0.020 0.001 PHE A 219 TRP 0.016 0.001 TRP A1044 HIS 0.010 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (33873) covalent geometry : angle 0.50613 / 0.27 (46153) hydrogen bonds : bond 0.03264 / 2.18 ( 1428) hydrogen bonds : angle 4.24339 / 2.99 ( 3970) metal coordination : bond 0.00363 / 0.20 ( 32) metal coordination : angle 2.62806 / 1.67 ( 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 420 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 368 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8125 (mt) REVERT: A 133 LYS cc_start: 0.9047 (mttm) cc_final: 0.8754 (mtmt) REVERT: A 277 GLU cc_start: 0.8735 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 293 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 320 ARG cc_start: 0.8328 (mtm110) cc_final: 0.8000 (mtm110) REVERT: A 330 LYS cc_start: 0.8643 (ptmt) cc_final: 0.8261 (pttm) REVERT: A 470 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8733 (pp) REVERT: A 856 THR cc_start: 0.9347 (m) cc_final: 0.8872 (p) REVERT: A 1217 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7526 (mmtm) REVERT: A 1225 PHE cc_start: 0.7638 (t80) cc_final: 0.7308 (t80) REVERT: A 1228 TRP cc_start: 0.8382 (p90) cc_final: 0.8114 (p90) REVERT: A 1265 ASN cc_start: 0.8279 (t0) cc_final: 0.7889 (m-40) REVERT: A 1411 GLU cc_start: 0.8653 (tp30) cc_final: 0.8316 (tp30) REVERT: B 72 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: B 272 THR cc_start: 0.9255 (m) cc_final: 0.8803 (p) REVERT: B 304 ASP cc_start: 0.8472 (t70) cc_final: 0.8211 (t70) REVERT: B 470 LYS cc_start: 0.9131 (mppt) cc_final: 0.8778 (ptmt) REVERT: B 595 ARG cc_start: 0.8894 (ttt180) cc_final: 0.8487 (tmm160) REVERT: B 598 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8303 (tm-30) REVERT: B 618 ASP cc_start: 0.8923 (t0) cc_final: 0.8356 (t70) REVERT: B 622 LYS cc_start: 0.8942 (mttt) cc_final: 0.8655 (mtmm) REVERT: B 629 ASP cc_start: 0.8619 (t0) cc_final: 0.8284 (p0) REVERT: B 1065 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: C 75 MET cc_start: 0.9060 (mmm) cc_final: 0.8688 (tpp) REVERT: C 94 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8178 (ttmm) REVERT: C 136 ASP cc_start: 0.7675 (t70) cc_final: 0.7390 (t0) REVERT: D 1 MET cc_start: 0.1120 (tmm) cc_final: -0.0736 (ttp) REVERT: D 66 ARG cc_start: 0.6444 (ttm170) cc_final: 0.6240 (mtp180) REVERT: E 6 GLU cc_start: 0.8780 (tp30) cc_final: 0.8419 (tp30) REVERT: E 50 MET cc_start: 0.8567 (ppp) cc_final: 0.8191 (ppp) REVERT: F 76 LYS cc_start: 0.9295 (tptt) cc_final: 0.9052 (tppp) REVERT: G 50 ASP cc_start: 0.7877 (t0) cc_final: 0.7512 (t0) REVERT: G 53 ASN cc_start: 0.9115 (t0) cc_final: 0.8805 (t0) REVERT: G 75 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7816 (mmm-85) REVERT: G 140 LYS cc_start: 0.6445 (mttt) cc_final: 0.5802 (tptm) REVERT: H 33 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7456 (tp40) REVERT: H 91 ASP cc_start: 0.8716 (m-30) cc_final: 0.8479 (m-30) REVERT: J 26 GLN cc_start: 0.8378 (tt0) cc_final: 0.8119 (mt0) REVERT: K 54 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8612 (mmm160) REVERT: L 68 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8416 (tt0) outliers start: 52 outliers final: 36 residues processed: 398 average time/residue: 0.2102 time to fit residues: 133.4606 Evaluate side-chains 384 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 247 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN D 150 ASN K 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087530 restraints weight = 50648.067| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.12 r_work: 0.2949 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33905 Z= 0.228 Angle : 0.578 13.391 46198 Z= 0.302 Chirality : 0.045 0.264 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.420 157.965 5346 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 1.49 % Allowed : 13.45 % Favored : 85.06 % 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: 0.37 (0.14), residues: 3854 helix: 1.48 (0.14), residues: 1342 sheet: -0.07 (0.21), residues: 618 loop : -0.50 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.017 0.001 TYR E 187 PHE 0.024 0.001 PHE A 219 TRP 0.013 0.001 TRP A1044 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (33873) covalent geometry : angle 0.56996 / 0.30 (46153) hydrogen bonds : bond 0.03792 / 2.52 ( 1428) hydrogen bonds : angle 4.40057 / 3.10 ( 3970) metal coordination : bond 0.00955 / 0.63 ( 32) metal coordination : angle 3.18974 / 2.00 ( 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 392 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 341 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8506 (pt) cc_final: 0.8201 (mt) REVERT: A 133 LYS cc_start: 0.9075 (mttm) cc_final: 0.8774 (mtmt) REVERT: A 277 GLU cc_start: 0.8745 (tt0) cc_final: 0.8091 (tm-30) REVERT: A 293 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 320 ARG cc_start: 0.8336 (mtm110) cc_final: 0.8077 (mtm110) REVERT: A 330 LYS cc_start: 0.8784 (ptmt) cc_final: 0.8392 (pttm) REVERT: A 470 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8799 (pp) REVERT: A 1199 ARG cc_start: 0.8430 (tpt-90) cc_final: 0.7929 (mtt90) REVERT: A 1217 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7535 (mmtm) REVERT: A 1225 PHE cc_start: 0.7707 (t80) cc_final: 0.7390 (t80) REVERT: A 1228 TRP cc_start: 0.8351 (p90) cc_final: 0.7986 (p90) REVERT: A 1265 ASN cc_start: 0.8275 (t0) cc_final: 0.7837 (m-40) REVERT: A 1411 GLU cc_start: 0.8686 (tp30) cc_final: 0.8152 (tp30) REVERT: B 272 THR cc_start: 0.9313 (m) cc_final: 0.8853 (p) REVERT: B 304 ASP cc_start: 0.8494 (t70) cc_final: 0.8162 (t70) REVERT: B 470 LYS cc_start: 0.9137 (mppt) cc_final: 0.8805 (ptmt) REVERT: B 595 ARG cc_start: 0.9008 (ttt180) cc_final: 0.8576 (tmm160) REVERT: B 598 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 618 ASP cc_start: 0.8954 (t0) cc_final: 0.8398 (t70) REVERT: B 622 LYS cc_start: 0.8955 (mttt) cc_final: 0.8668 (mtmm) REVERT: B 904 ARG cc_start: 0.8246 (mtp180) cc_final: 0.8043 (mtp85) REVERT: B 1065 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: C 75 MET cc_start: 0.9121 (mmm) cc_final: 0.8772 (tpp) REVERT: C 94 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8186 (ttmm) REVERT: C 136 ASP cc_start: 0.7756 (t70) cc_final: 0.7469 (t0) REVERT: D 1 MET cc_start: 0.0975 (tmm) cc_final: -0.1015 (ttp) REVERT: D 66 ARG cc_start: 0.6649 (ttm170) cc_final: 0.6324 (mtp180) REVERT: E 50 MET cc_start: 0.8570 (ppp) cc_final: 0.8192 (ppp) REVERT: F 76 LYS cc_start: 0.9328 (tptt) cc_final: 0.9090 (tppp) REVERT: G 50 ASP cc_start: 0.7905 (t0) cc_final: 0.7552 (t0) REVERT: G 53 ASN cc_start: 0.9139 (t0) cc_final: 0.8829 (t0) REVERT: G 75 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7949 (mmm-85) REVERT: G 140 LYS cc_start: 0.6345 (mttt) cc_final: 0.5919 (tptm) REVERT: H 33 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7553 (tp40) REVERT: H 91 ASP cc_start: 0.8710 (m-30) cc_final: 0.8467 (m-30) REVERT: J 26 GLN cc_start: 0.8405 (tt0) cc_final: 0.8144 (mt0) REVERT: K 54 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.8593 (mmm160) REVERT: L 68 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8432 (tt0) outliers start: 51 outliers final: 45 residues processed: 369 average time/residue: 0.2313 time to fit residues: 136.9204 Evaluate side-chains 384 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.4980 chunk 268 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 232 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 314 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 321 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089827 restraints weight = 50363.918| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.16 r_work: 0.3046 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33905 Z= 0.106 Angle : 0.517 8.941 46198 Z= 0.274 Chirality : 0.042 0.272 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.344 156.288 5346 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 1.31 % Allowed : 13.69 % Favored : 85.00 % 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: 1.64 (0.15), residues: 1339 sheet: -0.02 (0.21), residues: 604 loop : -0.44 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 77 TYR 0.017 0.001 TYR E 187 PHE 0.020 0.001 PHE A 219 TRP 0.016 0.001 TRP A1044 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (33873) covalent geometry : angle 0.51093 / 0.27 (46153) hydrogen bonds : bond 0.03269 / 2.18 ( 1428) hydrogen bonds : angle 4.23247 / 2.98 ( 3970) metal coordination : bond 0.00397 / 0.23 ( 32) metal coordination : angle 2.60264 / 1.66 ( 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 395 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8388 (pt) cc_final: 0.8106 (mt) REVERT: A 133 LYS cc_start: 0.8995 (mttm) cc_final: 0.8768 (mtmt) REVERT: A 277 GLU cc_start: 0.8715 (tt0) cc_final: 0.8072 (tm-30) REVERT: A 293 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 330 LYS cc_start: 0.8677 (ptmt) cc_final: 0.8315 (pttm) REVERT: A 470 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8738 (pp) REVERT: A 856 THR cc_start: 0.9319 (m) cc_final: 0.8915 (p) REVERT: A 1199 ARG cc_start: 0.8555 (tpt-90) cc_final: 0.8062 (mtt90) REVERT: A 1215 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7695 (mmm160) REVERT: A 1217 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7482 (mmtm) REVERT: A 1225 PHE cc_start: 0.7682 (t80) cc_final: 0.7346 (t80) REVERT: A 1228 TRP cc_start: 0.8351 (p90) cc_final: 0.7944 (p90) REVERT: A 1265 ASN cc_start: 0.8334 (t0) cc_final: 0.7917 (m-40) REVERT: A 1411 GLU cc_start: 0.8671 (tp30) cc_final: 0.8365 (tp30) REVERT: B 272 THR cc_start: 0.9283 (m) cc_final: 0.8846 (p) REVERT: B 304 ASP cc_start: 0.8477 (t70) cc_final: 0.8228 (t70) REVERT: B 470 LYS cc_start: 0.9122 (mppt) cc_final: 0.8791 (ptmt) REVERT: B 595 ARG cc_start: 0.8900 (ttt180) cc_final: 0.8538 (tmm160) REVERT: B 598 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8294 (tm-30) REVERT: B 618 ASP cc_start: 0.8922 (t0) cc_final: 0.8393 (t70) REVERT: B 622 LYS cc_start: 0.8990 (mttt) cc_final: 0.8714 (mtmm) REVERT: B 629 ASP cc_start: 0.8689 (t0) cc_final: 0.8335 (p0) REVERT: B 1065 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: C 75 MET cc_start: 0.9058 (mmm) cc_final: 0.8717 (tpp) REVERT: C 94 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8206 (ttmm) REVERT: C 136 ASP cc_start: 0.7700 (t70) cc_final: 0.7440 (t0) REVERT: D 1 MET cc_start: 0.0677 (tmm) cc_final: -0.1260 (ttp) REVERT: E 50 MET cc_start: 0.8654 (ppp) cc_final: 0.8291 (ppp) REVERT: F 76 LYS cc_start: 0.9301 (tptt) cc_final: 0.9061 (tppp) REVERT: G 50 ASP cc_start: 0.7859 (t0) cc_final: 0.7511 (t0) REVERT: G 53 ASN cc_start: 0.9147 (t0) cc_final: 0.8836 (t0) REVERT: G 75 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7844 (mmm-85) REVERT: G 140 LYS cc_start: 0.6421 (mttt) cc_final: 0.5783 (tptm) REVERT: H 33 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7494 (tp40) REVERT: H 91 ASP cc_start: 0.8647 (m-30) cc_final: 0.8424 (m-30) REVERT: J 26 GLN cc_start: 0.8373 (tt0) cc_final: 0.8150 (mt0) REVERT: K 54 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8585 (mmm160) REVERT: L 68 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8432 (tt0) outliers start: 45 outliers final: 36 residues processed: 375 average time/residue: 0.1981 time to fit residues: 117.9610 Evaluate side-chains 383 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 374 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 343 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.083921 restraints weight = 50819.244| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.06 r_work: 0.2944 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 33905 Z= 0.419 Angle : 0.724 11.246 46198 Z= 0.373 Chirality : 0.050 0.272 5190 Planarity : 0.005 0.048 5630 Dihedral : 16.537 158.676 5346 Min Nonbonded Distance : 1.250 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 1.43 % Allowed : 13.60 % Favored : 84.97 % 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: 0.06 (0.13), residues: 3854 helix: 1.21 (0.14), residues: 1341 sheet: -0.28 (0.21), residues: 623 loop : -0.65 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 335 TYR 0.017 0.002 TYR E 187 PHE 0.028 0.002 PHE A 219 TRP 0.018 0.002 TRP B 561 HIS 0.011 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01008 / 0.42 (33873) covalent geometry : angle 0.71217 / 0.37 (46153) hydrogen bonds : bond 0.04626 / 3.06 ( 1428) hydrogen bonds : angle 4.70090 / 3.32 ( 3970) metal coordination : bond 0.01703 / 1.14 ( 32) metal coordination : angle 4.18189 / 2.59 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8609.25 seconds wall clock time: 148 minutes 2.26 seconds (8882.26 seconds total)