Starting phenix.real_space_refine on Sun Aug 9 09:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbm_54731/08_2026/9sbm_54731.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbm_54731/08_2026/9sbm_54731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sbm_54731/08_2026/9sbm_54731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbm_54731/08_2026/9sbm_54731.map" model { file = "/net/cci-nas-00/data/ceres_data/9sbm_54731/08_2026/9sbm_54731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbm_54731/08_2026/9sbm_54731.cif" } resolution = 4.17 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= 0.022 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 96 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20457 2.51 5 N 5734 2.21 5 O 6423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 32901 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10859 Classifications: {'peptide': 1379} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1316} Chain breaks: 11 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 breaks: 1 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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ATP:plan-1': 1, 'ATP:plan-2': 1} Unresolved non-hydrogen planarities: 13 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 67 108.190 68.952 95.038 1.00225.76 S ATOM 479 SG CYS A 70 107.854 65.938 92.756 1.00227.18 S ATOM 532 SG CYS A 77 105.110 68.490 92.834 1.00225.83 S ATOM 762 SG CYS A 107 83.045 74.625 135.667 1.00245.72 S ATOM 786 SG CYS A 110 83.999 71.178 136.040 1.00234.79 S ATOM 1091 SG CYS A 148 80.982 72.288 137.990 1.00246.94 S ATOM 1105 SG CYS A 167 84.405 73.669 139.024 1.00254.67 S ATOM 19520 SG CYS B1163 99.996 56.625 104.851 1.00224.44 S ATOM 19538 SG CYS B1166 98.190 59.962 104.810 1.00223.95 S ATOM 19663 SG CYS B1182 101.943 59.879 104.722 1.00232.74 S ATOM 19682 SG CYS B1185 100.149 58.949 107.910 1.00240.41 S ATOM 20670 SG CYS C 86 94.469 75.019 27.374 1.00273.11 S ATOM 20687 SG CYS C 88 97.529 77.641 27.984 1.00292.94 S ATOM 20720 SG CYS C 92 95.626 77.907 25.074 1.00252.63 S ATOM 20743 SG CYS C 95 93.693 78.633 28.064 1.00245.16 S ATOM 28328 SG CYS I 7 38.139 127.294 125.830 1.00388.62 S ATOM 28353 SG CYS I 10 41.967 127.226 126.143 1.00386.56 S ATOM 28519 SG CYS I 29 39.900 124.301 127.359 1.00431.94 S ATOM 28543 SG CYS I 32 39.754 127.481 129.278 1.00407.92 S ATOM 28870 SG CYS I 75 17.198 119.375 86.871 1.00464.88 S ATOM 28892 SG CYS I 78 17.371 122.967 85.708 1.00455.35 S ATOM 29108 SG CYS I 103 20.400 120.718 85.223 1.00438.88 S ATOM 29128 SG CYS I 106 19.343 121.674 88.762 1.00446.00 S ATOM 29230 SG CYS J 7 65.097 90.455 38.145 1.00188.94 S ATOM 29253 SG CYS J 10 65.216 88.585 34.857 1.00194.11 S ATOM 29533 SG CYS J 45 61.947 89.651 36.406 1.00191.68 S ATOM 29539 SG CYS J 46 64.182 92.172 34.665 1.00218.86 S ATOM 30662 SG CYS L 31 98.071 114.376 55.163 1.00381.59 S ATOM 30682 SG CYS L 34 99.114 115.679 51.812 1.00348.88 S ATOM 30786 SG CYS L 48 101.656 114.956 54.659 1.00377.91 S ATOM 30809 SG CYS L 51 99.545 117.998 54.836 1.00383.41 S Time building chain proxies: 6.05, per 1000 atoms: 0.18 Number of scatterers: 32901 At special positions: 0 Unit cell: (154.505, 156.681, 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 96 15.00 Mg 1 11.99 O 6423 8.00 N 5734 7.00 C 20457 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 49 sheets defined 39.4% alpha, 19.5% beta 39 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 3.99 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 104 removed outlier: 3.515A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.719A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.902A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.801A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.547A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.621A 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 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.606A 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: 3.550A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.607A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.889A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.532A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.720A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (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: 4.166A 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 996 removed outlier: 3.677A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 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 1173 Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1271 removed outlier: 3.810A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.414A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 4.001A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1447 through 1453 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.745A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.626A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 160 through 164 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: 3.636A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 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 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.500A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.754A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 4.562A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.511A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.552A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.563A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.993A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.676A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.925A pdb=" N TYR B 785 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.415A pdb=" N TYR B 811 " --> 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: 4.607A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.861A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.583A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (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 removed outlier: 3.548A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.562A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (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 4 through 26 removed outlier: 3.547A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.638A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) 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 157 through 169 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 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.519A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.604A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.060A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.582A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.619A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 62' Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.605A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU K 51 " --> pdb=" O ARG K 47 " (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: 9.642A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.892A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.524A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.556A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.823A 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: 3.573A 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: 7.079A 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 removed outlier: 3.519A pdb=" N GLY A 766 " --> pdb=" O VAL A 800 " (cutoff:3.500A) 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 removed outlier: 3.525A pdb=" N LEU A1306 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1227 removed outlier: 4.261A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A1150 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS I 46 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.512A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.512A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.853A 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 71 removed outlier: 3.720A pdb=" N ILE B 90 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.893A 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 71 removed outlier: 3.720A pdb=" N ILE B 90 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 130 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 165 " --> pdb=" O VAL B 130 " (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 125 through 126 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.550A pdb=" N VAL B 211 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.183A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.875A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.514A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 585 through 590 removed outlier: 6.630A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.033A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.033A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 821 through 825 removed outlier: 8.997A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET B 839 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR B 994 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N MET B 841 " --> pdb=" O TYR B 994 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (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: 3.608A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.538A pdb=" N PHE B1001 " --> pdb=" O TYR B1073 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.731A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.635A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 51 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE5, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.930A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.057A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.223A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR H 115 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.283A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE I 86 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 1362 hydrogen bonds defined for protein. 3729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 10.01 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10401 1.33 - 1.46: 5536 1.46 - 1.58: 17254 1.58 - 1.70: 187 1.70 - 1.82: 292 Bond restraints: 33670 Sorted by residual: bond pdb=" O5' ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.579 1.509 0.070 1.10e-02 8.26e+03 4.03e+01 bond pdb=" C1' DC T 32 " pdb=" N1 DC T 32 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.01e+01 bond pdb=" C1' DC T 22 " pdb=" N1 DC T 22 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.99e+01 bond pdb=" C1' DC N 73 " pdb=" N1 DC N 73 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" C1' DT T 30 " pdb=" N1 DT T 30 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.92e+01 ... (remaining 33665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 45602 3.25 - 6.49: 198 6.49 - 9.74: 41 9.74 - 12.98: 1 12.98 - 16.23: 2 Bond angle restraints: 45844 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 123.64 16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" PA ATP B1301 " pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " ideal model delta sigma weight residual 136.83 123.45 13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " ideal model delta sigma weight residual 101.57 109.29 -7.72 1.54e+00 4.24e-01 2.53e+01 angle pdb=" C THR A 709 " pdb=" N LEU A 710 " pdb=" CA LEU A 710 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" O2G ATP B1301 " pdb=" PG ATP B1301 " pdb=" O3B ATP B1301 " ideal model delta sigma weight residual 104.48 109.61 -5.13 1.14e+00 7.76e-01 2.05e+01 ... (remaining 45839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 19368 26.84 - 53.68: 762 53.68 - 80.53: 199 80.53 - 107.37: 10 107.37 - 134.21: 5 Dihedral angle restraints: 20344 sinusoidal: 9046 harmonic: 11298 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 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLU A 398 " pdb=" C GLU A 398 " pdb=" N HIS A 399 " pdb=" CA HIS A 399 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 20341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3693 0.039 - 0.078: 1019 0.078 - 0.116: 381 0.116 - 0.155: 55 0.155 - 0.194: 8 Chirality restraints: 5156 Sorted by residual: chirality pdb=" C3' DA T 40 " pdb=" C4' DA T 40 " pdb=" O3' DA T 40 " pdb=" C2' DA T 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CB ILE G 56 " pdb=" CA ILE G 56 " pdb=" CG1 ILE G 56 " pdb=" CG2 ILE G 56 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.11e-01 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 -2.44 -0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 5153 not shown) Planarity restraints: 5604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 710 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 170 " -0.017 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP C 170 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 170 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 170 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 170 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 170 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 51 " -0.023 2.00e-02 2.50e+03 9.67e-03 2.80e+00 pdb=" N9 DG N 51 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG N 51 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG N 51 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 51 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG N 51 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG N 51 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG N 51 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG N 51 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N 51 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG N 51 " 0.001 2.00e-02 2.50e+03 ... (remaining 5601 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 579 2.62 - 3.19: 31056 3.19 - 3.76: 53607 3.76 - 4.33: 72660 4.33 - 4.90: 114943 Nonbonded interactions: 272845 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 2.055 2.170 nonbonded pdb=" OG1 THR H 100 " pdb=" OD1 ASN H 139 " model vdw 2.079 3.040 nonbonded pdb=" NZ LYS E 122 " pdb=" OP1 DC T 29 " model vdw 2.137 3.120 nonbonded pdb=" OG SER E 157 " pdb=" OE1 GLU E 160 " model vdw 2.158 3.040 nonbonded pdb=" OG SER A 23 " pdb=" OE1 GLU A 25 " model vdw 2.169 3.040 ... (remaining 272840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 38.530 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.005 0.117 33702 Z= 0.302 Angle : 0.654 16.231 45889 Z= 0.415 Chirality : 0.042 0.194 5156 Planarity : 0.003 0.040 5604 Dihedral : 14.698 134.211 13024 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 0.03 % Allowed : 0.12 % Favored : 99.85 % 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: 0.86 (0.14), residues: 3833 helix: 1.96 (0.15), residues: 1296 sheet: 0.14 (0.21), residues: 601 loop : -0.19 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.016 0.001 TYR B 351 PHE 0.015 0.001 PHE I 4 TRP 0.035 0.002 TRP C 170 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.30 (33670) covalent geometry : angle 0.64190 / 0.41 (45844) hydrogen bonds : bond 0.20114 / 13.31 ( 1422) hydrogen bonds : angle 6.97604 / 4.92 ( 3933) metal coordination : bond 0.00808 / 0.51 ( 32) metal coordination : angle 4.11692 / 2.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 669 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8483 (mtt) cc_final: 0.8066 (mmt) REVERT: A 103 CYS cc_start: 0.9469 (m) cc_final: 0.9257 (m) REVERT: A 122 MET cc_start: 0.9770 (tpp) cc_final: 0.9510 (tpp) REVERT: A 124 GLN cc_start: 0.9696 (mt0) cc_final: 0.9399 (mt0) REVERT: A 177 ASP cc_start: 0.9373 (t0) cc_final: 0.9158 (m-30) REVERT: A 234 MET cc_start: 0.9146 (ttm) cc_final: 0.8885 (ttm) REVERT: A 449 SER cc_start: 0.8986 (m) cc_final: 0.8740 (p) REVERT: A 456 MET cc_start: 0.9225 (mtm) cc_final: 0.8798 (mtm) REVERT: A 470 LEU cc_start: 0.9431 (pp) cc_final: 0.9226 (pp) REVERT: A 487 MET cc_start: 0.9401 (mtp) cc_final: 0.9095 (mtm) REVERT: A 511 ILE cc_start: 0.9498 (mt) cc_final: 0.9268 (tp) REVERT: A 521 MET cc_start: 0.8966 (mtt) cc_final: 0.8558 (ptp) REVERT: A 526 ASP cc_start: 0.8729 (m-30) cc_final: 0.7370 (m-30) REVERT: A 746 MET cc_start: 0.9461 (mtm) cc_final: 0.9200 (mtp) REVERT: A 748 MET cc_start: 0.9224 (mtm) cc_final: 0.8474 (mpp) REVERT: A 818 MET cc_start: 0.9075 (mtp) cc_final: 0.8842 (mtp) REVERT: A 847 ASP cc_start: 0.8480 (p0) cc_final: 0.8280 (p0) REVERT: A 849 MET cc_start: 0.8363 (ttp) cc_final: 0.7362 (ttp) REVERT: A 873 MET cc_start: 0.9296 (mmp) cc_final: 0.8971 (mmp) REVERT: A 874 ASP cc_start: 0.9397 (t70) cc_final: 0.9045 (p0) REVERT: A 884 ASP cc_start: 0.8653 (m-30) cc_final: 0.8407 (m-30) REVERT: A 945 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9126 (mt-10) REVERT: A 1019 CYS cc_start: 0.9447 (m) cc_final: 0.9167 (m) REVERT: A 1062 GLU cc_start: 0.9259 (tp30) cc_final: 0.8896 (mm-30) REVERT: A 1063 MET cc_start: 0.9461 (mmm) cc_final: 0.9055 (mmt) REVERT: A 1209 MET cc_start: 0.8331 (mmp) cc_final: 0.7977 (mmp) REVERT: A 1268 LEU cc_start: 0.9076 (mt) cc_final: 0.8531 (mt) REVERT: A 1277 GLU cc_start: 0.9316 (tt0) cc_final: 0.9114 (tp30) REVERT: A 1280 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8178 (mp0) REVERT: A 1284 MET cc_start: 0.8982 (ttm) cc_final: 0.8536 (ttt) REVERT: A 1285 MET cc_start: 0.8433 (mmt) cc_final: 0.8162 (mmm) REVERT: A 1337 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9054 (pt0) REVERT: A 1373 ASP cc_start: 0.9398 (m-30) cc_final: 0.9149 (m-30) REVERT: A 1403 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6716 (mm-30) REVERT: A 1417 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7726 (mp0) REVERT: B 101 MET cc_start: 0.9620 (mtt) cc_final: 0.9376 (mtp) REVERT: B 216 GLU cc_start: 0.8975 (tt0) cc_final: 0.8597 (tp30) REVERT: B 224 GLN cc_start: 0.9437 (mt0) cc_final: 0.9194 (mp10) REVERT: B 228 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9031 (ttpt) REVERT: B 239 GLU cc_start: 0.9417 (pt0) cc_final: 0.8960 (pm20) REVERT: B 255 GLN cc_start: 0.9345 (pt0) cc_final: 0.8980 (pm20) REVERT: B 299 GLU cc_start: 0.9351 (tt0) cc_final: 0.8989 (mt-10) REVERT: B 301 ILE cc_start: 0.9627 (mt) cc_final: 0.9342 (mt) REVERT: B 394 ASP cc_start: 0.9122 (t0) cc_final: 0.8854 (p0) REVERT: B 451 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8894 (ptmt) REVERT: B 492 LEU cc_start: 0.9664 (mt) cc_final: 0.9454 (mt) REVERT: B 526 GLU cc_start: 0.8912 (tt0) cc_final: 0.8066 (mt-10) REVERT: B 542 MET cc_start: 0.8679 (mtm) cc_final: 0.8414 (mmm) REVERT: B 552 MET cc_start: 0.9531 (mmm) cc_final: 0.9183 (mmp) REVERT: B 563 MET cc_start: 0.9317 (ttp) cc_final: 0.9068 (ttp) REVERT: B 615 MET cc_start: 0.9106 (mtm) cc_final: 0.8395 (ptt) REVERT: B 697 GLU cc_start: 0.9347 (tt0) cc_final: 0.8675 (mt-10) REVERT: B 705 MET cc_start: 0.9003 (tpt) cc_final: 0.8767 (tpt) REVERT: B 762 ASN cc_start: 0.9115 (m-40) cc_final: 0.8839 (m-40) REVERT: B 773 MET cc_start: 0.9206 (mtt) cc_final: 0.8923 (mtt) REVERT: B 775 LYS cc_start: 0.9595 (mtmt) cc_final: 0.9310 (mtmm) REVERT: B 895 ASP cc_start: 0.8241 (m-30) cc_final: 0.7643 (t0) REVERT: B 904 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8124 (ttm170) REVERT: B 910 VAL cc_start: 0.8924 (t) cc_final: 0.8402 (p) REVERT: B 1021 MET cc_start: 0.9343 (mtm) cc_final: 0.8509 (ptp) REVERT: B 1032 SER cc_start: 0.9832 (m) cc_final: 0.9512 (p) REVERT: B 1082 MET cc_start: 0.9547 (tpp) cc_final: 0.8795 (tpp) REVERT: B 1095 LEU cc_start: 0.9522 (mt) cc_final: 0.9209 (mp) REVERT: B 1133 MET cc_start: 0.8462 (mtp) cc_final: 0.7943 (mtp) REVERT: B 1156 ASP cc_start: 0.5307 (m-30) cc_final: 0.5057 (p0) REVERT: C 40 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7680 (mt-10) REVERT: D 56 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7703 (ptm-80) REVERT: D 214 LEU cc_start: 0.8002 (pp) cc_final: 0.7708 (pp) REVERT: E 57 MET cc_start: 0.9098 (mtm) cc_final: 0.8816 (ptp) REVERT: E 93 MET cc_start: 0.8631 (tpp) cc_final: 0.8164 (tpt) REVERT: E 98 ILE cc_start: 0.9740 (mt) cc_final: 0.9398 (tp) REVERT: E 121 MET cc_start: 0.9643 (mtm) cc_final: 0.9442 (mpp) REVERT: E 123 LEU cc_start: 0.9677 (tp) cc_final: 0.8992 (tp) REVERT: E 144 ILE cc_start: 0.9480 (pt) cc_final: 0.9207 (mp) REVERT: E 177 ARG cc_start: 0.9342 (mtt180) cc_final: 0.9097 (ptp90) REVERT: E 203 GLU cc_start: 0.9386 (pt0) cc_final: 0.9142 (pm20) REVERT: F 87 LYS cc_start: 0.9529 (ptpt) cc_final: 0.9289 (ptpp) REVERT: F 88 TYR cc_start: 0.9202 (m-80) cc_final: 0.8660 (m-80) REVERT: F 93 ILE cc_start: 0.9668 (pt) cc_final: 0.9403 (pt) REVERT: F 119 ARG cc_start: 0.9518 (tpp80) cc_final: 0.9277 (mmm-85) REVERT: F 123 LYS cc_start: 0.9482 (tttm) cc_final: 0.9150 (tttt) REVERT: F 124 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8469 (tt0) REVERT: F 136 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8544 (mtt90) REVERT: G 14 HIS cc_start: 0.8430 (t-90) cc_final: 0.7892 (t-90) REVERT: G 60 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8744 (tmm-80) REVERT: G 61 ILE cc_start: 0.8640 (mt) cc_final: 0.8438 (mm) REVERT: G 62 LEU cc_start: 0.8551 (mt) cc_final: 0.8334 (mt) REVERT: G 75 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7872 (ttm-80) REVERT: G 115 MET cc_start: 0.3645 (mtp) cc_final: 0.3389 (mtp) REVERT: H 14 GLU cc_start: 0.8815 (tt0) cc_final: 0.8415 (tm-30) REVERT: H 26 ILE cc_start: 0.9260 (pt) cc_final: 0.8429 (pt) REVERT: H 27 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8709 (mp0) REVERT: H 42 ILE cc_start: 0.9504 (mm) cc_final: 0.9175 (mm) REVERT: H 123 MET cc_start: 0.9387 (ttt) cc_final: 0.8899 (tmm) REVERT: I 13 MET cc_start: 0.6178 (ptt) cc_final: 0.5367 (ppp) REVERT: I 17 ARG cc_start: 0.8310 (ttt180) cc_final: 0.7714 (tpp-160) REVERT: I 27 PHE cc_start: 0.8530 (m-80) cc_final: 0.8046 (m-80) REVERT: I 68 LEU cc_start: 0.9207 (mt) cc_final: 0.8675 (pp) REVERT: I 97 MET cc_start: 0.8547 (mtp) cc_final: 0.7577 (mmt) REVERT: J 49 MET cc_start: 0.9556 (tpp) cc_final: 0.9116 (tpp) REVERT: K 6 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7861 (mmm-85) REVERT: K 16 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7021 (mt-10) REVERT: K 17 SER cc_start: 0.9203 (m) cc_final: 0.8269 (p) REVERT: K 19 LEU cc_start: 0.9443 (mt) cc_final: 0.8912 (mt) REVERT: K 36 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8673 (mp0) REVERT: K 42 LEU cc_start: 0.9587 (tp) cc_final: 0.9343 (tp) REVERT: K 76 GLN cc_start: 0.9502 (tt0) cc_final: 0.9150 (tm-30) REVERT: L 56 LEU cc_start: 0.9036 (mt) cc_final: 0.8468 (mm) REVERT: L 66 GLN cc_start: 0.8739 (tt0) cc_final: 0.8175 (tm-30) REVERT: L 67 PHE cc_start: 0.7794 (m-80) cc_final: 0.7048 (m-80) outliers start: 1 outliers final: 0 residues processed: 670 average time/residue: 0.2226 time to fit residues: 237.4208 Evaluate side-chains 446 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN C 203 GLN D 9 GLN D 138 ASN H 137 GLN K 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.045724 restraints weight = 144598.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.047070 restraints weight = 80642.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.047983 restraints weight = 54821.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.048576 restraints weight = 42336.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.048963 restraints weight = 35810.994| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33702 Z= 0.230 Angle : 0.697 13.731 45889 Z= 0.361 Chirality : 0.046 0.239 5156 Planarity : 0.005 0.059 5604 Dihedral : 17.066 134.265 5256 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % 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: 0.52 (0.14), residues: 3833 helix: 1.60 (0.14), residues: 1320 sheet: -0.06 (0.21), residues: 610 loop : -0.37 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 30 TYR 0.017 0.002 TYR I 34 PHE 0.023 0.002 PHE B 322 TRP 0.023 0.002 TRP C 170 HIS 0.009 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (33670) covalent geometry : angle 0.67620 / 0.36 (45844) hydrogen bonds : bond 0.05186 / 3.39 ( 1422) hydrogen bonds : angle 5.52289 / 3.95 ( 3933) metal coordination : bond 0.00880 / 0.55 ( 32) metal coordination : angle 5.47986 / 4.00 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 511 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8548 (mtt) cc_final: 0.8327 (mmt) REVERT: A 108 MET cc_start: 0.9317 (mmm) cc_final: 0.9046 (mmm) REVERT: A 437 MET cc_start: 0.8786 (mmt) cc_final: 0.8031 (mmp) REVERT: A 444 PHE cc_start: 0.8929 (t80) cc_final: 0.7716 (t80) REVERT: A 449 SER cc_start: 0.9098 (m) cc_final: 0.8734 (p) REVERT: A 450 LEU cc_start: 0.9267 (mp) cc_final: 0.8823 (mm) REVERT: A 456 MET cc_start: 0.9518 (mtm) cc_final: 0.9123 (mtm) REVERT: A 487 MET cc_start: 0.8964 (mtp) cc_final: 0.8163 (mtm) REVERT: A 511 ILE cc_start: 0.9511 (mt) cc_final: 0.9217 (tp) REVERT: A 676 MET cc_start: 0.9108 (mmt) cc_final: 0.8868 (mmp) REVERT: A 746 MET cc_start: 0.9353 (mtm) cc_final: 0.9086 (mtp) REVERT: A 818 MET cc_start: 0.9071 (mtp) cc_final: 0.8780 (mtp) REVERT: A 849 MET cc_start: 0.8814 (ttp) cc_final: 0.7749 (ttp) REVERT: A 873 MET cc_start: 0.9411 (mmp) cc_final: 0.9086 (mmm) REVERT: A 1062 GLU cc_start: 0.8758 (tp30) cc_final: 0.8556 (mm-30) REVERT: A 1063 MET cc_start: 0.9410 (mmm) cc_final: 0.9023 (mmt) REVERT: A 1209 MET cc_start: 0.8528 (mmp) cc_final: 0.8112 (mmm) REVERT: A 1280 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8135 (mp0) REVERT: A 1284 MET cc_start: 0.8820 (ttm) cc_final: 0.8351 (ttt) REVERT: A 1285 MET cc_start: 0.8771 (mmt) cc_final: 0.8487 (mmm) REVERT: A 1373 ASP cc_start: 0.9158 (m-30) cc_final: 0.8909 (m-30) REVERT: A 1444 MET cc_start: 0.8326 (mmm) cc_final: 0.8055 (mmt) REVERT: B 145 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8082 (ttp80) REVERT: B 199 MET cc_start: 0.8322 (mmp) cc_final: 0.8048 (mmp) REVERT: B 224 GLN cc_start: 0.9307 (mt0) cc_final: 0.9056 (mm110) REVERT: B 228 LYS cc_start: 0.9359 (mmmt) cc_final: 0.9126 (ttpt) REVERT: B 239 GLU cc_start: 0.9106 (pt0) cc_final: 0.8832 (pm20) REVERT: B 255 GLN cc_start: 0.9341 (pt0) cc_final: 0.8867 (pm20) REVERT: B 299 GLU cc_start: 0.9056 (tt0) cc_final: 0.8702 (mt-10) REVERT: B 310 MET cc_start: 0.9292 (mtp) cc_final: 0.9084 (mtp) REVERT: B 531 GLN cc_start: 0.8884 (pm20) cc_final: 0.8100 (tm-30) REVERT: B 563 MET cc_start: 0.8966 (ttp) cc_final: 0.8670 (ttp) REVERT: B 698 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8565 (mt-10) REVERT: B 762 ASN cc_start: 0.9117 (m-40) cc_final: 0.8539 (m-40) REVERT: B 775 LYS cc_start: 0.9520 (mtmt) cc_final: 0.9243 (mtmm) REVERT: B 809 MET cc_start: 0.8998 (mtp) cc_final: 0.8622 (mtp) REVERT: B 895 ASP cc_start: 0.8245 (m-30) cc_final: 0.7869 (t0) REVERT: B 910 VAL cc_start: 0.9212 (t) cc_final: 0.8704 (p) REVERT: B 999 MET cc_start: 0.9344 (tpp) cc_final: 0.8976 (tpp) REVERT: B 1032 SER cc_start: 0.9751 (m) cc_final: 0.9398 (p) REVERT: B 1095 LEU cc_start: 0.9751 (mt) cc_final: 0.9529 (mp) REVERT: B 1111 MET cc_start: 0.9127 (mmm) cc_final: 0.8729 (mmm) REVERT: B 1133 MET cc_start: 0.8930 (mtp) cc_final: 0.8351 (mtp) REVERT: B 1169 MET cc_start: 0.8788 (mpp) cc_final: 0.8419 (mpp) REVERT: C 40 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 56 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7910 (ptm-80) REVERT: E 22 MET cc_start: 0.9293 (tmm) cc_final: 0.9062 (tmm) REVERT: E 98 ILE cc_start: 0.9674 (mt) cc_final: 0.9438 (tp) REVERT: E 123 LEU cc_start: 0.9685 (tp) cc_final: 0.9450 (tp) REVERT: E 144 ILE cc_start: 0.9501 (pt) cc_final: 0.9192 (mp) REVERT: E 179 GLN cc_start: 0.8744 (mp10) cc_final: 0.8234 (mp10) REVERT: E 215 MET cc_start: 0.8758 (ppp) cc_final: 0.8459 (ppp) REVERT: F 88 TYR cc_start: 0.9069 (m-80) cc_final: 0.8372 (m-80) REVERT: F 89 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8702 (mt-10) REVERT: F 94 LEU cc_start: 0.9482 (mm) cc_final: 0.9237 (mm) REVERT: F 119 ARG cc_start: 0.9415 (tpp80) cc_final: 0.9093 (mmm-85) REVERT: F 122 MET cc_start: 0.9264 (mtp) cc_final: 0.8963 (mtm) REVERT: F 123 LYS cc_start: 0.9621 (tttm) cc_final: 0.9284 (tttt) REVERT: G 1 MET cc_start: 0.9481 (mmm) cc_final: 0.8916 (tpt) REVERT: G 14 HIS cc_start: 0.8512 (t-90) cc_final: 0.8070 (t-90) REVERT: H 26 ILE cc_start: 0.9475 (pt) cc_final: 0.8403 (pt) REVERT: H 27 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8746 (mp0) REVERT: H 40 LEU cc_start: 0.9582 (tp) cc_final: 0.9328 (tp) REVERT: H 42 ILE cc_start: 0.9619 (mm) cc_final: 0.9368 (mm) REVERT: I 13 MET cc_start: 0.7118 (ptt) cc_final: 0.6042 (ppp) REVERT: I 27 PHE cc_start: 0.8395 (m-80) cc_final: 0.7722 (m-80) REVERT: I 34 TYR cc_start: 0.8300 (t80) cc_final: 0.7605 (t80) REVERT: I 80 SER cc_start: 0.6376 (t) cc_final: 0.6159 (t) REVERT: I 87 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7734 (mm-40) REVERT: I 97 MET cc_start: 0.8493 (mtp) cc_final: 0.7882 (mmt) REVERT: J 21 TYR cc_start: 0.9627 (t80) cc_final: 0.9399 (t80) REVERT: J 32 GLU cc_start: 0.8629 (pm20) cc_final: 0.8210 (pm20) REVERT: K 6 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8198 (mmm-85) REVERT: K 38 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8830 (mm-30) REVERT: K 41 THR cc_start: 0.9246 (m) cc_final: 0.9031 (p) REVERT: K 49 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8663 (tm-30) REVERT: K 77 THR cc_start: 0.9410 (p) cc_final: 0.8755 (t) REVERT: L 57 LEU cc_start: 0.9123 (mp) cc_final: 0.8722 (mp) REVERT: L 66 GLN cc_start: 0.8663 (tt0) cc_final: 0.8349 (tm-30) REVERT: L 67 PHE cc_start: 0.8453 (m-80) cc_final: 0.7576 (m-10) outliers start: 2 outliers final: 0 residues processed: 513 average time/residue: 0.2080 time to fit residues: 174.0208 Evaluate side-chains 403 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 296 optimal weight: 9.9990 chunk 335 optimal weight: 0.0040 chunk 310 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 251 optimal weight: 0.0000 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 344 optimal weight: 8.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1432 GLN B 733 HIS B 740 HIS B 951 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS G 153 GLN H 11 GLN J 53 HIS K 104 ASN K 110 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.046918 restraints weight = 141134.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.048289 restraints weight = 78295.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.049153 restraints weight = 52551.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049797 restraints weight = 40660.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.050186 restraints weight = 34150.446| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33702 Z= 0.140 Angle : 0.600 10.466 45889 Z= 0.315 Chirality : 0.044 0.236 5156 Planarity : 0.004 0.049 5604 Dihedral : 16.936 133.597 5256 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % 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: 0.45 (0.14), residues: 3833 helix: 1.53 (0.14), residues: 1327 sheet: -0.17 (0.21), residues: 606 loop : -0.37 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 852 TYR 0.033 0.001 TYR B 797 PHE 0.017 0.001 PHE K 71 TRP 0.015 0.001 TRP C 170 HIS 0.010 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (33670) covalent geometry : angle 0.58619 / 0.31 (45844) hydrogen bonds : bond 0.04235 / 2.77 ( 1422) hydrogen bonds : angle 5.01534 / 3.60 ( 3933) metal coordination : bond 0.00647 / 0.39 ( 32) metal coordination : angle 4.13884 / 2.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 513 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4166 (tmm) cc_final: 0.2920 (tmm) REVERT: A 108 MET cc_start: 0.9271 (mmm) cc_final: 0.9014 (mmm) REVERT: A 222 LEU cc_start: 0.9636 (mt) cc_final: 0.9382 (mt) REVERT: A 436 ILE cc_start: 0.9647 (pt) cc_final: 0.9389 (mm) REVERT: A 456 MET cc_start: 0.9543 (mtm) cc_final: 0.9118 (mtm) REVERT: A 511 ILE cc_start: 0.9457 (mt) cc_final: 0.9191 (mt) REVERT: A 549 MET cc_start: 0.9505 (mmm) cc_final: 0.9122 (mmm) REVERT: A 676 MET cc_start: 0.9058 (mmt) cc_final: 0.8837 (mmp) REVERT: A 746 MET cc_start: 0.9294 (mtm) cc_final: 0.8979 (mtp) REVERT: A 818 MET cc_start: 0.9048 (mtp) cc_final: 0.8781 (mtp) REVERT: A 849 MET cc_start: 0.8866 (ttp) cc_final: 0.7854 (ttp) REVERT: A 873 MET cc_start: 0.9324 (mmp) cc_final: 0.8963 (mmp) REVERT: A 1063 MET cc_start: 0.9366 (mmm) cc_final: 0.9062 (mmt) REVERT: A 1209 MET cc_start: 0.8533 (mmp) cc_final: 0.8205 (mmm) REVERT: A 1280 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8139 (mp0) REVERT: A 1284 MET cc_start: 0.8685 (ttm) cc_final: 0.8251 (ttt) REVERT: A 1285 MET cc_start: 0.8728 (mmt) cc_final: 0.8458 (mmm) REVERT: A 1373 ASP cc_start: 0.9152 (m-30) cc_final: 0.8814 (m-30) REVERT: A 1444 MET cc_start: 0.8287 (mmm) cc_final: 0.7279 (mtp) REVERT: B 101 MET cc_start: 0.9425 (mtp) cc_final: 0.9190 (mtp) REVERT: B 145 ARG cc_start: 0.8430 (mtp180) cc_final: 0.8047 (ttp80) REVERT: B 228 LYS cc_start: 0.9329 (mmmt) cc_final: 0.9119 (ttpt) REVERT: B 239 GLU cc_start: 0.9021 (pt0) cc_final: 0.8705 (pm20) REVERT: B 255 GLN cc_start: 0.9308 (pt0) cc_final: 0.8878 (pm20) REVERT: B 299 GLU cc_start: 0.8987 (tt0) cc_final: 0.8701 (mt-10) REVERT: B 301 ILE cc_start: 0.9657 (mt) cc_final: 0.9031 (pt) REVERT: B 303 TYR cc_start: 0.7952 (m-80) cc_final: 0.7706 (m-80) REVERT: B 489 SER cc_start: 0.9495 (p) cc_final: 0.9261 (t) REVERT: B 531 GLN cc_start: 0.8824 (pm20) cc_final: 0.8142 (tm-30) REVERT: B 615 MET cc_start: 0.8886 (ptp) cc_final: 0.8550 (pmm) REVERT: B 697 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 698 GLU cc_start: 0.9352 (mt-10) cc_final: 0.8559 (mt-10) REVERT: B 762 ASN cc_start: 0.9001 (m-40) cc_final: 0.8494 (m-40) REVERT: B 789 MET cc_start: 0.8628 (mmp) cc_final: 0.8373 (mmm) REVERT: B 796 LEU cc_start: 0.9188 (tp) cc_final: 0.8873 (mt) REVERT: B 809 MET cc_start: 0.8952 (mtp) cc_final: 0.8648 (mtp) REVERT: B 895 ASP cc_start: 0.8345 (m-30) cc_final: 0.7768 (t0) REVERT: B 910 VAL cc_start: 0.9194 (t) cc_final: 0.8678 (p) REVERT: B 999 MET cc_start: 0.9317 (tpp) cc_final: 0.8939 (tpp) REVERT: B 1032 SER cc_start: 0.9741 (m) cc_final: 0.9373 (p) REVERT: B 1095 LEU cc_start: 0.9773 (mt) cc_final: 0.9571 (mp) REVERT: B 1111 MET cc_start: 0.9081 (mmm) cc_final: 0.8740 (mmm) REVERT: B 1133 MET cc_start: 0.8934 (mtp) cc_final: 0.8441 (mtp) REVERT: B 1169 MET cc_start: 0.8764 (mpp) cc_final: 0.8418 (mpp) REVERT: B 1206 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9135 (tt0) REVERT: B 1208 MET cc_start: 0.9424 (mtm) cc_final: 0.9206 (mtm) REVERT: C 40 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 163 ILE cc_start: 0.9558 (pt) cc_final: 0.9213 (mp) REVERT: D 56 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7925 (ptm-80) REVERT: D 70 PHE cc_start: 0.7976 (m-80) cc_final: 0.7616 (m-80) REVERT: D 156 ASP cc_start: 0.7767 (p0) cc_final: 0.7458 (p0) REVERT: E 22 MET cc_start: 0.9275 (tmm) cc_final: 0.9027 (tmm) REVERT: E 98 ILE cc_start: 0.9647 (mt) cc_final: 0.9406 (tp) REVERT: E 121 MET cc_start: 0.9497 (mmm) cc_final: 0.9193 (mpp) REVERT: E 144 ILE cc_start: 0.9489 (pt) cc_final: 0.9158 (mp) REVERT: E 179 GLN cc_start: 0.8864 (mp10) cc_final: 0.8285 (mp10) REVERT: E 215 MET cc_start: 0.8739 (ppp) cc_final: 0.8411 (ppp) REVERT: F 84 TYR cc_start: 0.9005 (m-80) cc_final: 0.8618 (m-80) REVERT: F 89 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9104 (mt-10) REVERT: F 119 ARG cc_start: 0.9380 (tpp80) cc_final: 0.8908 (mmm-85) REVERT: F 123 LYS cc_start: 0.9588 (tttm) cc_final: 0.9058 (tttt) REVERT: F 124 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8179 (mm-30) REVERT: G 1 MET cc_start: 0.9531 (mmm) cc_final: 0.8871 (tpt) REVERT: G 14 HIS cc_start: 0.8501 (t-90) cc_final: 0.8002 (t-90) REVERT: G 51 TYR cc_start: 0.7802 (t80) cc_final: 0.7591 (t80) REVERT: G 60 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8714 (mmt-90) REVERT: H 26 ILE cc_start: 0.9521 (pt) cc_final: 0.9014 (pt) REVERT: H 40 LEU cc_start: 0.9578 (tp) cc_final: 0.9301 (tp) REVERT: H 42 ILE cc_start: 0.9593 (mm) cc_final: 0.9388 (mm) REVERT: H 123 MET cc_start: 0.9013 (tmm) cc_final: 0.8509 (tmm) REVERT: H 146 ARG cc_start: 0.8405 (ttm110) cc_final: 0.7785 (mtp180) REVERT: I 13 MET cc_start: 0.7046 (ptt) cc_final: 0.6003 (ppp) REVERT: I 17 ARG cc_start: 0.8353 (ttt180) cc_final: 0.7378 (tpp-160) REVERT: I 27 PHE cc_start: 0.8526 (m-80) cc_final: 0.7915 (m-80) REVERT: I 30 ARG cc_start: 0.8359 (ptp90) cc_final: 0.7782 (ptp90) REVERT: I 34 TYR cc_start: 0.8299 (t80) cc_final: 0.7677 (t80) REVERT: I 45 ARG cc_start: 0.8219 (ttt90) cc_final: 0.7960 (ttt90) REVERT: I 87 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7407 (mm-40) REVERT: I 97 MET cc_start: 0.8313 (mtp) cc_final: 0.7879 (mmt) REVERT: J 32 GLU cc_start: 0.8772 (pm20) cc_final: 0.8209 (pm20) REVERT: J 58 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8632 (mm-30) REVERT: K 6 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: K 41 THR cc_start: 0.9268 (m) cc_final: 0.8963 (p) REVERT: K 49 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8667 (tm-30) REVERT: K 77 THR cc_start: 0.9248 (p) cc_final: 0.8935 (t) REVERT: L 49 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8107 (pptt) REVERT: L 67 PHE cc_start: 0.8339 (m-80) cc_final: 0.7600 (m-80) outliers start: 2 outliers final: 0 residues processed: 514 average time/residue: 0.2127 time to fit residues: 177.7521 Evaluate side-chains 411 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 294 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 368 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 281 optimal weight: 40.0000 chunk 133 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1432 GLN B 415 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 101 GLN G 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.045995 restraints weight = 144232.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.047337 restraints weight = 80515.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048233 restraints weight = 55028.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.048834 restraints weight = 42650.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.049221 restraints weight = 36101.379| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33702 Z= 0.187 Angle : 0.613 14.942 45889 Z= 0.317 Chirality : 0.043 0.236 5156 Planarity : 0.004 0.047 5604 Dihedral : 16.943 134.627 5256 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % 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: 0.38 (0.14), residues: 3833 helix: 1.50 (0.14), residues: 1327 sheet: -0.31 (0.21), residues: 608 loop : -0.40 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 731 TYR 0.021 0.001 TYR J 21 PHE 0.017 0.001 PHE E 96 TRP 0.010 0.001 TRP A1044 HIS 0.007 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (33670) covalent geometry : angle 0.59610 / 0.32 (45844) hydrogen bonds : bond 0.03983 / 2.62 ( 1422) hydrogen bonds : angle 4.94685 / 3.55 ( 3933) metal coordination : bond 0.00682 / 0.44 ( 32) metal coordination : angle 4.62201 / 3.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 487 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4280 (tmm) cc_final: 0.2957 (tmm) REVERT: A 108 MET cc_start: 0.9310 (mmm) cc_final: 0.9047 (mmm) REVERT: A 222 LEU cc_start: 0.9723 (mt) cc_final: 0.9483 (mt) REVERT: A 436 ILE cc_start: 0.9660 (pt) cc_final: 0.9425 (mm) REVERT: A 511 ILE cc_start: 0.9524 (mt) cc_final: 0.9077 (mt) REVERT: A 521 MET cc_start: 0.9099 (ptp) cc_final: 0.8897 (pmm) REVERT: A 549 MET cc_start: 0.9526 (mmm) cc_final: 0.9217 (mmm) REVERT: A 746 MET cc_start: 0.9280 (mtm) cc_final: 0.8998 (mtp) REVERT: A 818 MET cc_start: 0.9026 (mtp) cc_final: 0.8755 (mtp) REVERT: A 833 GLU cc_start: 0.8472 (pm20) cc_final: 0.8221 (pm20) REVERT: A 849 MET cc_start: 0.8776 (ttp) cc_final: 0.8087 (ttp) REVERT: A 873 MET cc_start: 0.9322 (mmp) cc_final: 0.8941 (mmm) REVERT: A 1063 MET cc_start: 0.9310 (mmm) cc_final: 0.8935 (mmm) REVERT: A 1209 MET cc_start: 0.8698 (mmp) cc_final: 0.8440 (mmp) REVERT: A 1280 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8077 (mp0) REVERT: A 1284 MET cc_start: 0.8623 (ttm) cc_final: 0.8162 (ttt) REVERT: A 1341 ILE cc_start: 0.9766 (tp) cc_final: 0.9478 (tp) REVERT: A 1373 ASP cc_start: 0.9163 (m-30) cc_final: 0.8822 (m-30) REVERT: A 1444 MET cc_start: 0.8331 (mmm) cc_final: 0.8034 (mmt) REVERT: B 101 MET cc_start: 0.9432 (mtp) cc_final: 0.9156 (mtp) REVERT: B 145 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8099 (ttp80) REVERT: B 173 MET cc_start: 0.9240 (ttp) cc_final: 0.8635 (tpp) REVERT: B 199 MET cc_start: 0.8254 (mmp) cc_final: 0.8043 (mmp) REVERT: B 239 GLU cc_start: 0.9039 (pt0) cc_final: 0.8735 (pm20) REVERT: B 255 GLN cc_start: 0.9282 (pt0) cc_final: 0.8881 (pm20) REVERT: B 301 ILE cc_start: 0.9651 (mt) cc_final: 0.9095 (pt) REVERT: B 303 TYR cc_start: 0.8033 (m-80) cc_final: 0.7722 (m-80) REVERT: B 427 ASP cc_start: 0.9325 (t70) cc_final: 0.9080 (t0) REVERT: B 489 SER cc_start: 0.9515 (p) cc_final: 0.9290 (t) REVERT: B 542 MET cc_start: 0.9137 (mmm) cc_final: 0.8883 (mmm) REVERT: B 697 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8325 (mm-30) REVERT: B 698 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 762 ASN cc_start: 0.9023 (m-40) cc_final: 0.8522 (m-40) REVERT: B 789 MET cc_start: 0.8820 (mmp) cc_final: 0.8403 (mmm) REVERT: B 809 MET cc_start: 0.8973 (mtp) cc_final: 0.8708 (mtp) REVERT: B 895 ASP cc_start: 0.8346 (m-30) cc_final: 0.7769 (t0) REVERT: B 910 VAL cc_start: 0.9226 (t) cc_final: 0.8718 (p) REVERT: B 999 MET cc_start: 0.9243 (tpp) cc_final: 0.8918 (tpp) REVERT: B 1032 SER cc_start: 0.9730 (m) cc_final: 0.9368 (p) REVERT: B 1082 MET cc_start: 0.9249 (tpp) cc_final: 0.8858 (tpp) REVERT: B 1111 MET cc_start: 0.9123 (mmm) cc_final: 0.8727 (mmm) REVERT: B 1133 MET cc_start: 0.8824 (mtp) cc_final: 0.8591 (mtp) REVERT: B 1169 MET cc_start: 0.8735 (mpp) cc_final: 0.8346 (mpp) REVERT: B 1208 MET cc_start: 0.9450 (mtm) cc_final: 0.9200 (mtm) REVERT: C 40 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 56 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7915 (ptm-80) REVERT: D 66 ARG cc_start: 0.7478 (ttm170) cc_final: 0.7247 (ttm170) REVERT: D 70 PHE cc_start: 0.8018 (m-80) cc_final: 0.7727 (m-80) REVERT: D 156 ASP cc_start: 0.7897 (p0) cc_final: 0.7613 (p0) REVERT: E 22 MET cc_start: 0.9311 (tmm) cc_final: 0.9080 (tmm) REVERT: E 50 MET cc_start: 0.8995 (pmm) cc_final: 0.8714 (pmm) REVERT: E 98 ILE cc_start: 0.9645 (mt) cc_final: 0.9382 (tp) REVERT: E 121 MET cc_start: 0.9511 (mmm) cc_final: 0.9206 (mpp) REVERT: E 179 GLN cc_start: 0.8898 (mp10) cc_final: 0.8633 (mp10) REVERT: E 215 MET cc_start: 0.8757 (ppp) cc_final: 0.8410 (ppp) REVERT: F 84 TYR cc_start: 0.8990 (m-80) cc_final: 0.8588 (m-80) REVERT: F 89 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9078 (mt-10) REVERT: F 119 ARG cc_start: 0.9378 (tpp80) cc_final: 0.9068 (mmm-85) REVERT: F 123 LYS cc_start: 0.9546 (tttm) cc_final: 0.9041 (tttt) REVERT: F 124 GLU cc_start: 0.8926 (tp30) cc_final: 0.8693 (tp30) REVERT: G 1 MET cc_start: 0.9527 (mmm) cc_final: 0.8835 (tpt) REVERT: G 9 LEU cc_start: 0.7687 (tp) cc_final: 0.7285 (mm) REVERT: G 14 HIS cc_start: 0.8477 (t-90) cc_final: 0.8052 (t-90) REVERT: G 58 ARG cc_start: 0.9063 (ptp-110) cc_final: 0.8618 (ptp-110) REVERT: G 60 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8664 (ttp80) REVERT: H 110 ASP cc_start: 0.9039 (p0) cc_final: 0.8722 (p0) REVERT: H 123 MET cc_start: 0.9110 (tmm) cc_final: 0.8670 (tmm) REVERT: I 9 ASP cc_start: 0.8915 (t70) cc_final: 0.8714 (t70) REVERT: I 13 MET cc_start: 0.7006 (ptt) cc_final: 0.5926 (ppp) REVERT: I 17 ARG cc_start: 0.8337 (ttt180) cc_final: 0.7364 (tpp-160) REVERT: I 27 PHE cc_start: 0.8441 (m-80) cc_final: 0.7950 (m-80) REVERT: I 30 ARG cc_start: 0.8337 (ptp90) cc_final: 0.7767 (ptp90) REVERT: I 87 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7363 (mm-40) REVERT: I 97 MET cc_start: 0.8316 (mtp) cc_final: 0.7968 (mmt) REVERT: J 29 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8397 (pp20) REVERT: J 49 MET cc_start: 0.9436 (tpp) cc_final: 0.8551 (tpp) REVERT: J 58 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8724 (mm-30) REVERT: K 6 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8080 (mmm-85) REVERT: K 41 THR cc_start: 0.9296 (m) cc_final: 0.9033 (p) REVERT: K 49 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8933 (tm-30) REVERT: K 76 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8269 (tm-30) REVERT: K 77 THR cc_start: 0.9255 (p) cc_final: 0.8949 (t) REVERT: L 49 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8106 (pptt) outliers start: 2 outliers final: 0 residues processed: 489 average time/residue: 0.1991 time to fit residues: 159.1238 Evaluate side-chains 396 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 293 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 289 optimal weight: 20.0000 chunk 331 optimal weight: 20.0000 chunk 237 optimal weight: 0.0670 chunk 16 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1432 GLN B 794 ASN B 951 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 63 ASN G 153 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.045746 restraints weight = 144712.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.047058 restraints weight = 79382.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.047912 restraints weight = 53730.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.048554 restraints weight = 41784.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.048909 restraints weight = 35232.306| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33702 Z= 0.204 Angle : 0.623 13.218 45889 Z= 0.322 Chirality : 0.043 0.235 5156 Planarity : 0.004 0.050 5604 Dihedral : 16.963 135.458 5256 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % 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: 0.35 (0.14), residues: 3833 helix: 1.48 (0.14), residues: 1326 sheet: -0.33 (0.21), residues: 608 loop : -0.43 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 91 TYR 0.032 0.001 TYR G 167 PHE 0.042 0.001 PHE I 4 TRP 0.016 0.001 TRP B 561 HIS 0.009 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (33670) covalent geometry : angle 0.60833 / 0.32 (45844) hydrogen bonds : bond 0.03888 / 2.56 ( 1422) hydrogen bonds : angle 4.90828 / 3.52 ( 3933) metal coordination : bond 0.00764 / 0.49 ( 32) metal coordination : angle 4.29333 / 2.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 474 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9391 (mmm) cc_final: 0.9098 (mmm) REVERT: A 122 MET cc_start: 0.9341 (ttm) cc_final: 0.9054 (ttm) REVERT: A 222 LEU cc_start: 0.9704 (mt) cc_final: 0.9443 (mt) REVERT: A 444 PHE cc_start: 0.9089 (t80) cc_final: 0.8328 (t80) REVERT: A 487 MET cc_start: 0.9143 (mtm) cc_final: 0.8794 (mtm) REVERT: A 511 ILE cc_start: 0.9525 (mt) cc_final: 0.9027 (mt) REVERT: A 521 MET cc_start: 0.9160 (ptp) cc_final: 0.8839 (pmm) REVERT: A 549 MET cc_start: 0.9546 (mmm) cc_final: 0.9334 (mmm) REVERT: A 746 MET cc_start: 0.9315 (mtm) cc_final: 0.9078 (mtt) REVERT: A 748 MET cc_start: 0.8833 (mpp) cc_final: 0.8588 (mpp) REVERT: A 818 MET cc_start: 0.9015 (mtp) cc_final: 0.8731 (mtp) REVERT: A 833 GLU cc_start: 0.8484 (pm20) cc_final: 0.8238 (pm20) REVERT: A 849 MET cc_start: 0.8799 (ttp) cc_final: 0.8133 (ttp) REVERT: A 873 MET cc_start: 0.9346 (mmp) cc_final: 0.8947 (mmm) REVERT: A 1063 MET cc_start: 0.9276 (mmm) cc_final: 0.8843 (mmm) REVERT: A 1280 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8093 (mp0) REVERT: A 1373 ASP cc_start: 0.9178 (m-30) cc_final: 0.8820 (m-30) REVERT: A 1418 LEU cc_start: 0.9270 (tp) cc_final: 0.9013 (tp) REVERT: A 1444 MET cc_start: 0.8371 (mmm) cc_final: 0.7285 (mtp) REVERT: B 101 MET cc_start: 0.9469 (mtp) cc_final: 0.9171 (mtp) REVERT: B 145 ARG cc_start: 0.8512 (mtp180) cc_final: 0.8137 (ttp80) REVERT: B 199 MET cc_start: 0.8392 (mmp) cc_final: 0.8157 (mmp) REVERT: B 239 GLU cc_start: 0.9084 (pt0) cc_final: 0.8739 (pm20) REVERT: B 255 GLN cc_start: 0.9316 (pt0) cc_final: 0.8898 (pm20) REVERT: B 301 ILE cc_start: 0.9651 (mt) cc_final: 0.9288 (mt) REVERT: B 303 TYR cc_start: 0.8066 (m-80) cc_final: 0.7695 (m-80) REVERT: B 427 ASP cc_start: 0.9393 (t70) cc_final: 0.9185 (t0) REVERT: B 432 MET cc_start: 0.9330 (mtm) cc_final: 0.8784 (ptp) REVERT: B 489 SER cc_start: 0.9498 (p) cc_final: 0.9282 (t) REVERT: B 531 GLN cc_start: 0.8843 (pm20) cc_final: 0.8194 (tm-30) REVERT: B 542 MET cc_start: 0.9189 (mmm) cc_final: 0.8838 (mmm) REVERT: B 552 MET cc_start: 0.8892 (mmp) cc_final: 0.8686 (mmp) REVERT: B 563 MET cc_start: 0.8852 (ttp) cc_final: 0.8596 (ttp) REVERT: B 697 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 698 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8557 (mt-10) REVERT: B 762 ASN cc_start: 0.9039 (m-40) cc_final: 0.8544 (m-40) REVERT: B 789 MET cc_start: 0.8878 (mmp) cc_final: 0.8473 (mmm) REVERT: B 809 MET cc_start: 0.8989 (mtp) cc_final: 0.8737 (mtp) REVERT: B 842 ASN cc_start: 0.9609 (t0) cc_final: 0.9370 (t0) REVERT: B 895 ASP cc_start: 0.8381 (m-30) cc_final: 0.7896 (t0) REVERT: B 910 VAL cc_start: 0.9266 (t) cc_final: 0.8747 (p) REVERT: B 999 MET cc_start: 0.9262 (tpp) cc_final: 0.8928 (tpp) REVERT: B 1032 SER cc_start: 0.9736 (m) cc_final: 0.9391 (p) REVERT: B 1082 MET cc_start: 0.9267 (tpp) cc_final: 0.8789 (tpp) REVERT: B 1169 MET cc_start: 0.8802 (mpp) cc_final: 0.8409 (mpp) REVERT: B 1208 MET cc_start: 0.9497 (mtm) cc_final: 0.9194 (mtm) REVERT: C 75 MET cc_start: 0.9302 (tpp) cc_final: 0.8891 (tpp) REVERT: D 56 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7882 (ptm-80) REVERT: D 66 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7194 (ttm170) REVERT: D 70 PHE cc_start: 0.7955 (m-80) cc_final: 0.7655 (m-80) REVERT: D 156 ASP cc_start: 0.8003 (p0) cc_final: 0.7714 (p0) REVERT: E 22 MET cc_start: 0.9384 (tmm) cc_final: 0.9129 (tmm) REVERT: E 50 MET cc_start: 0.8999 (pmm) cc_final: 0.8782 (pmm) REVERT: E 98 ILE cc_start: 0.9660 (mt) cc_final: 0.9405 (tp) REVERT: E 121 MET cc_start: 0.9511 (mmm) cc_final: 0.9235 (mpp) REVERT: E 179 GLN cc_start: 0.8937 (mp10) cc_final: 0.8462 (mp10) REVERT: E 215 MET cc_start: 0.8811 (ppp) cc_final: 0.8346 (ppp) REVERT: F 89 GLU cc_start: 0.9439 (mt-10) cc_final: 0.8951 (mt-10) REVERT: F 119 ARG cc_start: 0.9412 (tpp80) cc_final: 0.8957 (mmm-85) REVERT: F 124 GLU cc_start: 0.9034 (tp30) cc_final: 0.8599 (tp30) REVERT: G 1 MET cc_start: 0.9518 (mmm) cc_final: 0.8827 (tpt) REVERT: G 6 ASP cc_start: 0.6865 (p0) cc_final: 0.6647 (p0) REVERT: G 9 LEU cc_start: 0.7648 (tp) cc_final: 0.7258 (mm) REVERT: G 14 HIS cc_start: 0.8490 (t-90) cc_final: 0.7954 (t-90) REVERT: G 58 ARG cc_start: 0.9087 (ptp-110) cc_final: 0.7675 (ptp-110) REVERT: G 60 ARG cc_start: 0.9084 (ttp80) cc_final: 0.8744 (mmt-90) REVERT: H 40 LEU cc_start: 0.9647 (tp) cc_final: 0.9376 (tp) REVERT: H 103 LYS cc_start: 0.9377 (tptt) cc_final: 0.9045 (tptm) REVERT: H 123 MET cc_start: 0.9119 (tmm) cc_final: 0.8641 (tmm) REVERT: I 9 ASP cc_start: 0.8949 (t70) cc_final: 0.8743 (t70) REVERT: I 13 MET cc_start: 0.7034 (ptt) cc_final: 0.5915 (ppp) REVERT: I 17 ARG cc_start: 0.8290 (ttt180) cc_final: 0.7411 (tpp-160) REVERT: I 27 PHE cc_start: 0.8538 (m-80) cc_final: 0.7937 (m-10) REVERT: I 30 ARG cc_start: 0.8344 (ptp90) cc_final: 0.7794 (ptp90) REVERT: I 36 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8207 (tm-30) REVERT: I 83 ASN cc_start: 0.7448 (p0) cc_final: 0.7213 (p0) REVERT: J 54 VAL cc_start: 0.9534 (t) cc_final: 0.9313 (m) REVERT: J 58 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8751 (mm-30) REVERT: K 6 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: K 49 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8979 (tm-30) REVERT: K 76 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8361 (tm-30) REVERT: L 49 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8133 (pptt) outliers start: 3 outliers final: 1 residues processed: 477 average time/residue: 0.2099 time to fit residues: 163.2328 Evaluate side-chains 386 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 88 optimal weight: 7.9990 chunk 368 optimal weight: 0.9980 chunk 358 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1258 HIS B 415 GLN ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 61 GLN E 101 GLN E 146 HIS G 153 GLN I 87 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.045882 restraints weight = 144504.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.047244 restraints weight = 80533.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048110 restraints weight = 54656.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.048690 restraints weight = 42546.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.049023 restraints weight = 36155.673| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33702 Z= 0.177 Angle : 0.607 12.051 45889 Z= 0.313 Chirality : 0.043 0.235 5156 Planarity : 0.004 0.060 5604 Dihedral : 16.966 135.809 5256 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 0.06 % Allowed : 1.37 % Favored : 98.57 % 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: 0.38 (0.14), residues: 3833 helix: 1.49 (0.14), residues: 1327 sheet: -0.29 (0.21), residues: 625 loop : -0.39 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 192 TYR 0.026 0.001 TYR G 167 PHE 0.015 0.001 PHE K 71 TRP 0.012 0.001 TRP B 561 HIS 0.010 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (33670) covalent geometry : angle 0.58903 / 0.31 (45844) hydrogen bonds : bond 0.03728 / 2.44 ( 1422) hydrogen bonds : angle 4.80763 / 3.45 ( 3933) metal coordination : bond 0.01100 / 0.77 ( 32) metal coordination : angle 4.65468 / 3.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 483 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9389 (mmm) cc_final: 0.9066 (mmm) REVERT: A 122 MET cc_start: 0.9298 (ttm) cc_final: 0.9043 (ttm) REVERT: A 146 MET cc_start: 0.9124 (mmm) cc_final: 0.8904 (mmm) REVERT: A 222 LEU cc_start: 0.9705 (mt) cc_final: 0.9429 (mt) REVERT: A 444 PHE cc_start: 0.9001 (t80) cc_final: 0.8234 (t80) REVERT: A 487 MET cc_start: 0.9165 (mtm) cc_final: 0.8609 (mtm) REVERT: A 511 ILE cc_start: 0.9496 (mt) cc_final: 0.8965 (mt) REVERT: A 521 MET cc_start: 0.9129 (ptp) cc_final: 0.8900 (pmm) REVERT: A 549 MET cc_start: 0.9520 (mmm) cc_final: 0.9115 (mmm) REVERT: A 676 MET cc_start: 0.8958 (mmt) cc_final: 0.8670 (mmp) REVERT: A 746 MET cc_start: 0.9277 (mtm) cc_final: 0.9007 (mtt) REVERT: A 818 MET cc_start: 0.8985 (mtp) cc_final: 0.8715 (mtp) REVERT: A 849 MET cc_start: 0.8752 (ttp) cc_final: 0.8210 (ttp) REVERT: A 873 MET cc_start: 0.9313 (mmp) cc_final: 0.8926 (mmm) REVERT: A 1063 MET cc_start: 0.9286 (mmm) cc_final: 0.8870 (mmm) REVERT: A 1280 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8099 (mp0) REVERT: A 1284 MET cc_start: 0.8707 (ttm) cc_final: 0.8309 (ttt) REVERT: A 1373 ASP cc_start: 0.9107 (m-30) cc_final: 0.8721 (m-30) REVERT: A 1444 MET cc_start: 0.8377 (mmm) cc_final: 0.7181 (mtp) REVERT: B 101 MET cc_start: 0.9440 (mtp) cc_final: 0.9158 (mtp) REVERT: B 145 ARG cc_start: 0.8512 (mtp180) cc_final: 0.8107 (ttp80) REVERT: B 173 MET cc_start: 0.9023 (ttp) cc_final: 0.8079 (tpp) REVERT: B 199 MET cc_start: 0.8408 (mmp) cc_final: 0.8166 (mmp) REVERT: B 239 GLU cc_start: 0.9014 (pt0) cc_final: 0.8701 (pm20) REVERT: B 255 GLN cc_start: 0.9292 (pt0) cc_final: 0.8894 (pm20) REVERT: B 301 ILE cc_start: 0.9676 (mt) cc_final: 0.9329 (mt) REVERT: B 303 TYR cc_start: 0.8088 (m-80) cc_final: 0.7721 (m-80) REVERT: B 432 MET cc_start: 0.9318 (mtm) cc_final: 0.8771 (ptp) REVERT: B 489 SER cc_start: 0.9508 (p) cc_final: 0.9279 (t) REVERT: B 531 GLN cc_start: 0.8822 (pm20) cc_final: 0.8234 (tm-30) REVERT: B 542 MET cc_start: 0.9187 (mmm) cc_final: 0.8818 (mmm) REVERT: B 697 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8409 (mt-10) REVERT: B 698 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 762 ASN cc_start: 0.9027 (m-40) cc_final: 0.8515 (m-40) REVERT: B 789 MET cc_start: 0.8900 (mmp) cc_final: 0.8509 (mmm) REVERT: B 809 MET cc_start: 0.8897 (mtp) cc_final: 0.8685 (mtp) REVERT: B 895 ASP cc_start: 0.8384 (m-30) cc_final: 0.7884 (p0) REVERT: B 910 VAL cc_start: 0.9255 (t) cc_final: 0.8742 (p) REVERT: B 997 GLU cc_start: 0.8766 (pm20) cc_final: 0.8561 (pm20) REVERT: B 1032 SER cc_start: 0.9725 (m) cc_final: 0.9358 (p) REVERT: B 1082 MET cc_start: 0.9229 (tpp) cc_final: 0.8637 (tpp) REVERT: B 1169 MET cc_start: 0.8840 (mpp) cc_final: 0.8411 (mpp) REVERT: B 1208 MET cc_start: 0.9470 (mtm) cc_final: 0.9132 (mtm) REVERT: C 40 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 75 MET cc_start: 0.9237 (tpp) cc_final: 0.8845 (tpp) REVERT: D 56 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7888 (ptm-80) REVERT: D 66 ARG cc_start: 0.7347 (ttm170) cc_final: 0.7143 (ttm170) REVERT: D 70 PHE cc_start: 0.8013 (m-80) cc_final: 0.7790 (m-80) REVERT: D 156 ASP cc_start: 0.8115 (p0) cc_final: 0.7879 (p0) REVERT: E 22 MET cc_start: 0.9353 (tmm) cc_final: 0.9122 (tmm) REVERT: E 50 MET cc_start: 0.9051 (pmm) cc_final: 0.8835 (pmm) REVERT: E 98 ILE cc_start: 0.9639 (mt) cc_final: 0.9383 (tp) REVERT: E 121 MET cc_start: 0.9511 (mmm) cc_final: 0.9252 (mpp) REVERT: E 179 GLN cc_start: 0.8892 (mp10) cc_final: 0.8495 (mp10) REVERT: E 215 MET cc_start: 0.8694 (ppp) cc_final: 0.8291 (ppp) REVERT: F 85 MET cc_start: 0.9324 (tmm) cc_final: 0.9048 (tmm) REVERT: F 89 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8865 (mt-10) REVERT: F 119 ARG cc_start: 0.9374 (tpp80) cc_final: 0.8903 (mmm-85) REVERT: F 124 GLU cc_start: 0.9010 (tp30) cc_final: 0.8594 (tp30) REVERT: G 1 MET cc_start: 0.9515 (mmm) cc_final: 0.8811 (tpt) REVERT: G 9 LEU cc_start: 0.7687 (tp) cc_final: 0.7285 (mm) REVERT: G 14 HIS cc_start: 0.8523 (t-90) cc_final: 0.7950 (t-90) REVERT: G 51 TYR cc_start: 0.7594 (t80) cc_final: 0.7341 (t80) REVERT: G 58 ARG cc_start: 0.9117 (ptp-110) cc_final: 0.7714 (ptp-110) REVERT: G 60 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8745 (mmt-90) REVERT: G 74 TYR cc_start: 0.8913 (p90) cc_final: 0.8699 (p90) REVERT: H 40 LEU cc_start: 0.9626 (tp) cc_final: 0.9396 (tp) REVERT: H 123 MET cc_start: 0.9128 (tmm) cc_final: 0.8576 (tmm) REVERT: I 2 THR cc_start: 0.7784 (t) cc_final: 0.7365 (m) REVERT: I 9 ASP cc_start: 0.9027 (t70) cc_final: 0.8818 (t70) REVERT: I 13 MET cc_start: 0.7073 (ptt) cc_final: 0.5987 (ppp) REVERT: I 17 ARG cc_start: 0.8330 (ttt180) cc_final: 0.7430 (tpp-160) REVERT: I 27 PHE cc_start: 0.8455 (m-80) cc_final: 0.7935 (m-10) REVERT: I 36 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8223 (tm-30) REVERT: I 81 ARG cc_start: 0.8095 (mpt180) cc_final: 0.7852 (mmt-90) REVERT: J 54 VAL cc_start: 0.9576 (t) cc_final: 0.9352 (m) REVERT: K 6 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: K 49 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8970 (tm-30) REVERT: K 76 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8323 (tm-30) REVERT: K 106 GLU cc_start: 0.8942 (tp30) cc_final: 0.8694 (tp30) REVERT: L 49 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8053 (pptt) outliers start: 2 outliers final: 0 residues processed: 484 average time/residue: 0.2053 time to fit residues: 163.1109 Evaluate side-chains 396 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 375 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 318 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 365 optimal weight: 0.0040 chunk 140 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 341 optimal weight: 0.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 124 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1258 HIS B 951 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN G 153 GLN L 66 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.046408 restraints weight = 143066.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.047773 restraints weight = 79575.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.048613 restraints weight = 53906.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.049239 restraints weight = 41957.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.049595 restraints weight = 35366.625| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33702 Z= 0.150 Angle : 0.598 17.583 45889 Z= 0.307 Chirality : 0.043 0.233 5156 Planarity : 0.004 0.047 5604 Dihedral : 16.946 135.839 5256 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.49 % Favored : 95.36 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.18 % 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: 0.42 (0.14), residues: 3833 helix: 1.51 (0.14), residues: 1329 sheet: -0.20 (0.21), residues: 617 loop : -0.40 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 969 TYR 0.023 0.001 TYR G 167 PHE 0.017 0.001 PHE B1146 TRP 0.013 0.001 TRP B 561 HIS 0.007 0.001 HIS C 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (33670) covalent geometry : angle 0.58424 / 0.31 (45844) hydrogen bonds : bond 0.03596 / 2.35 ( 1422) hydrogen bonds : angle 4.73043 / 3.39 ( 3933) metal coordination : bond 0.00742 / 0.49 ( 32) metal coordination : angle 4.08533 / 2.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 486 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9380 (mmm) cc_final: 0.9069 (mmm) REVERT: A 122 MET cc_start: 0.9265 (ttm) cc_final: 0.9022 (ttm) REVERT: A 222 LEU cc_start: 0.9717 (mt) cc_final: 0.9447 (mt) REVERT: A 444 PHE cc_start: 0.8999 (t80) cc_final: 0.8146 (t80) REVERT: A 511 ILE cc_start: 0.9489 (mt) cc_final: 0.9205 (mt) REVERT: A 676 MET cc_start: 0.9020 (mmt) cc_final: 0.8761 (mmp) REVERT: A 746 MET cc_start: 0.9280 (mtm) cc_final: 0.9006 (mtt) REVERT: A 818 MET cc_start: 0.8991 (mtp) cc_final: 0.8717 (mtp) REVERT: A 849 MET cc_start: 0.8738 (ttp) cc_final: 0.8144 (ttp) REVERT: A 873 MET cc_start: 0.9303 (mmp) cc_final: 0.8795 (mmp) REVERT: A 1063 MET cc_start: 0.9303 (mmm) cc_final: 0.8899 (mmm) REVERT: A 1209 MET cc_start: 0.8118 (mmp) cc_final: 0.7812 (mmp) REVERT: A 1280 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8113 (mp0) REVERT: A 1284 MET cc_start: 0.8708 (ttm) cc_final: 0.8325 (ttt) REVERT: A 1368 MET cc_start: 0.9376 (mtp) cc_final: 0.9172 (mtp) REVERT: A 1373 ASP cc_start: 0.9109 (m-30) cc_final: 0.8688 (m-30) REVERT: A 1444 MET cc_start: 0.8369 (mmm) cc_final: 0.7125 (mtp) REVERT: B 101 MET cc_start: 0.9437 (mtp) cc_final: 0.9151 (mtp) REVERT: B 145 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8128 (ttp80) REVERT: B 199 MET cc_start: 0.8447 (mmp) cc_final: 0.8166 (mmp) REVERT: B 239 GLU cc_start: 0.9019 (pt0) cc_final: 0.8685 (pm20) REVERT: B 255 GLN cc_start: 0.9289 (pt0) cc_final: 0.8869 (pm20) REVERT: B 301 ILE cc_start: 0.9662 (mt) cc_final: 0.9296 (mt) REVERT: B 303 TYR cc_start: 0.8066 (m-80) cc_final: 0.7676 (m-80) REVERT: B 432 MET cc_start: 0.9313 (mtm) cc_final: 0.8761 (ptp) REVERT: B 489 SER cc_start: 0.9508 (p) cc_final: 0.9278 (t) REVERT: B 531 GLN cc_start: 0.8868 (pm20) cc_final: 0.8290 (tm-30) REVERT: B 542 MET cc_start: 0.9218 (mmm) cc_final: 0.8822 (mmm) REVERT: B 697 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 698 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8550 (mt-10) REVERT: B 762 ASN cc_start: 0.9041 (m-40) cc_final: 0.8533 (m-40) REVERT: B 789 MET cc_start: 0.8870 (mmp) cc_final: 0.8527 (mmm) REVERT: B 895 ASP cc_start: 0.8374 (m-30) cc_final: 0.7881 (p0) REVERT: B 910 VAL cc_start: 0.9244 (t) cc_final: 0.8738 (p) REVERT: B 1032 SER cc_start: 0.9739 (m) cc_final: 0.9361 (p) REVERT: B 1072 MET cc_start: 0.8025 (ttm) cc_final: 0.7768 (ttm) REVERT: B 1082 MET cc_start: 0.9250 (tpp) cc_final: 0.8624 (tpp) REVERT: B 1169 MET cc_start: 0.8876 (mpp) cc_final: 0.8452 (mpp) REVERT: B 1208 MET cc_start: 0.9484 (mtm) cc_final: 0.9146 (mtm) REVERT: C 75 MET cc_start: 0.9248 (tpp) cc_final: 0.8891 (tpp) REVERT: C 163 ILE cc_start: 0.9599 (pt) cc_final: 0.9239 (mp) REVERT: D 56 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7863 (ptm-80) REVERT: D 66 ARG cc_start: 0.7273 (ttm170) cc_final: 0.7061 (ttm170) REVERT: D 70 PHE cc_start: 0.8095 (m-80) cc_final: 0.7875 (m-80) REVERT: D 156 ASP cc_start: 0.8152 (p0) cc_final: 0.7912 (p0) REVERT: D 190 GLU cc_start: 0.7067 (pt0) cc_final: 0.6677 (tm-30) REVERT: E 22 MET cc_start: 0.9340 (tmm) cc_final: 0.9131 (tmm) REVERT: E 98 ILE cc_start: 0.9648 (mt) cc_final: 0.9397 (tp) REVERT: E 179 GLN cc_start: 0.8906 (mp10) cc_final: 0.8670 (mp10) REVERT: E 215 MET cc_start: 0.8690 (ppp) cc_final: 0.8354 (ppp) REVERT: F 85 MET cc_start: 0.9352 (tmm) cc_final: 0.9062 (tmm) REVERT: F 89 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8832 (mt-10) REVERT: F 124 GLU cc_start: 0.9001 (tp30) cc_final: 0.8624 (tp30) REVERT: G 1 MET cc_start: 0.9524 (mmm) cc_final: 0.8782 (tpt) REVERT: G 14 HIS cc_start: 0.8539 (t-90) cc_final: 0.7959 (t-90) REVERT: G 51 TYR cc_start: 0.7655 (t80) cc_final: 0.7400 (t80) REVERT: G 58 ARG cc_start: 0.9110 (ptp-110) cc_final: 0.7727 (ptp-110) REVERT: G 60 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8743 (mmt-90) REVERT: H 40 LEU cc_start: 0.9629 (tp) cc_final: 0.9404 (tp) REVERT: H 103 LYS cc_start: 0.9340 (tptt) cc_final: 0.8973 (tptm) REVERT: H 123 MET cc_start: 0.9207 (tmm) cc_final: 0.8615 (tmm) REVERT: I 2 THR cc_start: 0.7515 (t) cc_final: 0.7176 (p) REVERT: I 9 ASP cc_start: 0.8947 (t70) cc_final: 0.8742 (t70) REVERT: I 13 MET cc_start: 0.7056 (ptt) cc_final: 0.6011 (ppp) REVERT: I 17 ARG cc_start: 0.8322 (ttt180) cc_final: 0.7399 (tpp-160) REVERT: I 27 PHE cc_start: 0.8515 (m-80) cc_final: 0.7945 (m-10) REVERT: I 73 ARG cc_start: 0.8561 (tmt170) cc_final: 0.8307 (tmt170) REVERT: I 87 GLN cc_start: 0.8375 (mt0) cc_final: 0.7495 (mt0) REVERT: J 34 THR cc_start: 0.8983 (p) cc_final: 0.8205 (p) REVERT: J 58 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8775 (mm-30) REVERT: K 6 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8017 (mmm-85) REVERT: K 49 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8995 (tm-30) REVERT: K 76 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8324 (tm-30) REVERT: K 106 GLU cc_start: 0.8969 (tp30) cc_final: 0.8705 (tp30) REVERT: L 49 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8078 (pptt) outliers start: 1 outliers final: 0 residues processed: 487 average time/residue: 0.2009 time to fit residues: 160.8591 Evaluate side-chains 401 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 204 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS E 61 GLN E 101 GLN G 153 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.046419 restraints weight = 144240.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.047738 restraints weight = 78641.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.048624 restraints weight = 52789.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.049262 restraints weight = 40761.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.049603 restraints weight = 34366.506| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33702 Z= 0.148 Angle : 0.594 16.193 45889 Z= 0.303 Chirality : 0.043 0.233 5156 Planarity : 0.004 0.045 5604 Dihedral : 16.932 136.108 5256 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.49 % Rotamer: Outliers : 0.03 % Allowed : 0.90 % Favored : 99.07 % 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: 0.42 (0.14), residues: 3833 helix: 1.52 (0.14), residues: 1333 sheet: -0.24 (0.21), residues: 611 loop : -0.39 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.025 0.001 TYR J 21 PHE 0.015 0.001 PHE K 71 TRP 0.011 0.001 TRP B 561 HIS 0.010 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (33670) covalent geometry : angle 0.57897 / 0.30 (45844) hydrogen bonds : bond 0.03521 / 2.30 ( 1422) hydrogen bonds : angle 4.66849 / 3.33 ( 3933) metal coordination : bond 0.00813 / 0.53 ( 32) metal coordination : angle 4.34752 / 2.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9396 (mmm) cc_final: 0.9092 (mmm) REVERT: A 222 LEU cc_start: 0.9720 (mt) cc_final: 0.9445 (mt) REVERT: A 444 PHE cc_start: 0.9013 (t80) cc_final: 0.8185 (t80) REVERT: A 487 MET cc_start: 0.9211 (mtm) cc_final: 0.8473 (mtm) REVERT: A 511 ILE cc_start: 0.9514 (mt) cc_final: 0.9165 (mt) REVERT: A 676 MET cc_start: 0.9054 (mmt) cc_final: 0.8811 (mmp) REVERT: A 746 MET cc_start: 0.9301 (mtm) cc_final: 0.9034 (mtp) REVERT: A 748 MET cc_start: 0.8923 (mpp) cc_final: 0.8611 (mpp) REVERT: A 818 MET cc_start: 0.8983 (mtp) cc_final: 0.8723 (mtp) REVERT: A 849 MET cc_start: 0.8715 (ttp) cc_final: 0.8229 (ttp) REVERT: A 873 MET cc_start: 0.9294 (mmp) cc_final: 0.8753 (mmp) REVERT: A 1063 MET cc_start: 0.9307 (mmm) cc_final: 0.8929 (mmm) REVERT: A 1280 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8123 (mp0) REVERT: A 1284 MET cc_start: 0.8697 (ttm) cc_final: 0.8345 (ttt) REVERT: A 1368 MET cc_start: 0.9405 (mtp) cc_final: 0.9130 (mtp) REVERT: A 1373 ASP cc_start: 0.9109 (m-30) cc_final: 0.8684 (m-30) REVERT: A 1444 MET cc_start: 0.8372 (mmm) cc_final: 0.7194 (mtp) REVERT: B 101 MET cc_start: 0.9466 (mtp) cc_final: 0.9157 (mtp) REVERT: B 145 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8160 (ttp80) REVERT: B 173 MET cc_start: 0.9210 (ttp) cc_final: 0.8825 (ttp) REVERT: B 199 MET cc_start: 0.8411 (mmp) cc_final: 0.8148 (mmp) REVERT: B 239 GLU cc_start: 0.9067 (pt0) cc_final: 0.8710 (pm20) REVERT: B 255 GLN cc_start: 0.9302 (pt0) cc_final: 0.8812 (pm20) REVERT: B 301 ILE cc_start: 0.9645 (mt) cc_final: 0.9322 (mt) REVERT: B 303 TYR cc_start: 0.8060 (m-80) cc_final: 0.7663 (m-80) REVERT: B 432 MET cc_start: 0.9313 (mtm) cc_final: 0.8768 (ptp) REVERT: B 489 SER cc_start: 0.9508 (p) cc_final: 0.9305 (t) REVERT: B 531 GLN cc_start: 0.8904 (pm20) cc_final: 0.8244 (tm-30) REVERT: B 542 MET cc_start: 0.9214 (mmm) cc_final: 0.8811 (mmm) REVERT: B 615 MET cc_start: 0.8448 (pmm) cc_final: 0.8240 (pmm) REVERT: B 697 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8356 (mt-10) REVERT: B 698 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8550 (mt-10) REVERT: B 762 ASN cc_start: 0.9036 (m-40) cc_final: 0.8563 (m-40) REVERT: B 789 MET cc_start: 0.8906 (mmp) cc_final: 0.8592 (mmm) REVERT: B 809 MET cc_start: 0.8962 (mtp) cc_final: 0.8731 (mtp) REVERT: B 895 ASP cc_start: 0.8367 (m-30) cc_final: 0.7871 (p0) REVERT: B 910 VAL cc_start: 0.9239 (t) cc_final: 0.8733 (p) REVERT: B 1013 ASN cc_start: 0.9137 (t0) cc_final: 0.8869 (t0) REVERT: B 1032 SER cc_start: 0.9732 (m) cc_final: 0.9359 (p) REVERT: B 1072 MET cc_start: 0.7997 (ttm) cc_final: 0.7760 (ttm) REVERT: B 1082 MET cc_start: 0.9310 (tpp) cc_final: 0.8584 (tpp) REVERT: C 75 MET cc_start: 0.9274 (tpp) cc_final: 0.8948 (tpp) REVERT: C 163 ILE cc_start: 0.9608 (pt) cc_final: 0.9212 (mp) REVERT: D 56 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7872 (ptm-80) REVERT: D 66 ARG cc_start: 0.7314 (ttm170) cc_final: 0.7087 (ttm170) REVERT: D 70 PHE cc_start: 0.8121 (m-80) cc_final: 0.7891 (m-80) REVERT: D 156 ASP cc_start: 0.8193 (p0) cc_final: 0.7882 (p0) REVERT: D 190 GLU cc_start: 0.7119 (pt0) cc_final: 0.6652 (tm-30) REVERT: E 22 MET cc_start: 0.9384 (tmm) cc_final: 0.9148 (tmm) REVERT: E 179 GLN cc_start: 0.8909 (mp10) cc_final: 0.8690 (mp10) REVERT: E 215 MET cc_start: 0.8757 (ppp) cc_final: 0.8440 (ppp) REVERT: F 89 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8962 (mt-10) REVERT: F 124 GLU cc_start: 0.9083 (tp30) cc_final: 0.8665 (tp30) REVERT: G 1 MET cc_start: 0.9552 (mmm) cc_final: 0.8767 (tpt) REVERT: G 14 HIS cc_start: 0.8540 (t-90) cc_final: 0.7950 (t-90) REVERT: G 51 TYR cc_start: 0.7675 (t80) cc_final: 0.7423 (t80) REVERT: G 58 ARG cc_start: 0.9054 (ptp-110) cc_final: 0.7725 (ptp-110) REVERT: G 60 ARG cc_start: 0.9053 (ttp80) cc_final: 0.8724 (mmt-90) REVERT: G 122 ASN cc_start: 0.7490 (t0) cc_final: 0.7218 (t0) REVERT: H 40 LEU cc_start: 0.9646 (tp) cc_final: 0.9421 (tp) REVERT: H 103 LYS cc_start: 0.9332 (tptt) cc_final: 0.8957 (tptm) REVERT: H 123 MET cc_start: 0.9212 (tmm) cc_final: 0.8417 (tmm) REVERT: I 2 THR cc_start: 0.7461 (t) cc_final: 0.7039 (p) REVERT: I 9 ASP cc_start: 0.8976 (t70) cc_final: 0.8773 (t70) REVERT: I 13 MET cc_start: 0.7069 (ptt) cc_final: 0.6005 (ppp) REVERT: I 17 ARG cc_start: 0.8325 (ttt180) cc_final: 0.7414 (tpp-160) REVERT: I 27 PHE cc_start: 0.8421 (m-80) cc_final: 0.7963 (m-10) REVERT: I 73 ARG cc_start: 0.8658 (tmt170) cc_final: 0.8418 (tmt170) REVERT: I 81 ARG cc_start: 0.8191 (mpt180) cc_final: 0.7967 (mmt-90) REVERT: I 87 GLN cc_start: 0.8629 (mt0) cc_final: 0.7830 (mt0) REVERT: I 97 MET cc_start: 0.8526 (mmm) cc_final: 0.7568 (mmt) REVERT: J 49 MET cc_start: 0.9482 (tpp) cc_final: 0.9049 (tpp) REVERT: K 6 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: K 49 GLU cc_start: 0.9273 (tm-30) cc_final: 0.9010 (tm-30) REVERT: K 76 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8310 (tm-30) REVERT: K 106 GLU cc_start: 0.9010 (tp30) cc_final: 0.8735 (tp30) REVERT: L 49 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8041 (pptt) outliers start: 1 outliers final: 0 residues processed: 478 average time/residue: 0.2035 time to fit residues: 158.6712 Evaluate side-chains 391 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 3 optimal weight: 0.9980 chunk 325 optimal weight: 9.9990 chunk 46 optimal weight: 0.0270 chunk 348 optimal weight: 3.9990 chunk 285 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1258 HIS B 415 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN C 188 HIS D 143 ASN E 61 GLN G 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.046450 restraints weight = 142816.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.047766 restraints weight = 79477.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048663 restraints weight = 54193.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.049245 restraints weight = 42037.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049591 restraints weight = 35690.820| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33702 Z= 0.148 Angle : 0.599 13.983 45889 Z= 0.306 Chirality : 0.043 0.259 5156 Planarity : 0.004 0.060 5604 Dihedral : 16.931 136.415 5256 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % 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: 0.43 (0.14), residues: 3833 helix: 1.52 (0.14), residues: 1333 sheet: -0.23 (0.21), residues: 614 loop : -0.38 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 8 TYR 0.018 0.001 TYR G 167 PHE 0.017 0.001 PHE B1146 TRP 0.013 0.001 TRP B 561 HIS 0.010 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (33670) covalent geometry : angle 0.58377 / 0.30 (45844) hydrogen bonds : bond 0.03490 / 2.27 ( 1422) hydrogen bonds : angle 4.65393 / 3.33 ( 3933) metal coordination : bond 0.00782 / 0.52 ( 32) metal coordination : angle 4.27771 / 2.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9401 (mmm) cc_final: 0.9092 (mmm) REVERT: A 222 LEU cc_start: 0.9722 (mt) cc_final: 0.9440 (mt) REVERT: A 444 PHE cc_start: 0.9014 (t80) cc_final: 0.8202 (t80) REVERT: A 487 MET cc_start: 0.9193 (mtm) cc_final: 0.8451 (mtm) REVERT: A 511 ILE cc_start: 0.9386 (mt) cc_final: 0.9169 (mt) REVERT: A 526 ASP cc_start: 0.7821 (m-30) cc_final: 0.7613 (m-30) REVERT: A 549 MET cc_start: 0.9607 (mmm) cc_final: 0.8953 (mmm) REVERT: A 676 MET cc_start: 0.9001 (mmt) cc_final: 0.8766 (mmp) REVERT: A 746 MET cc_start: 0.9294 (mtm) cc_final: 0.9052 (mtt) REVERT: A 748 MET cc_start: 0.8830 (mpp) cc_final: 0.8547 (mpp) REVERT: A 818 MET cc_start: 0.8968 (mtp) cc_final: 0.8710 (mtp) REVERT: A 849 MET cc_start: 0.8746 (ttp) cc_final: 0.8194 (ttp) REVERT: A 873 MET cc_start: 0.9295 (mmp) cc_final: 0.8693 (mmp) REVERT: A 1063 MET cc_start: 0.9314 (mmm) cc_final: 0.8921 (mmm) REVERT: A 1280 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8128 (mp0) REVERT: A 1284 MET cc_start: 0.8684 (ttm) cc_final: 0.8281 (ttt) REVERT: A 1368 MET cc_start: 0.9399 (mtp) cc_final: 0.9072 (mtp) REVERT: A 1373 ASP cc_start: 0.9116 (m-30) cc_final: 0.8678 (m-30) REVERT: A 1444 MET cc_start: 0.8364 (mmm) cc_final: 0.7187 (mtp) REVERT: B 101 MET cc_start: 0.9458 (mtp) cc_final: 0.9153 (mtp) REVERT: B 145 ARG cc_start: 0.8570 (mtp180) cc_final: 0.8200 (ttp80) REVERT: B 173 MET cc_start: 0.9246 (ttp) cc_final: 0.8832 (ttp) REVERT: B 199 MET cc_start: 0.8450 (mmp) cc_final: 0.8184 (mmp) REVERT: B 239 GLU cc_start: 0.9071 (pt0) cc_final: 0.8707 (pm20) REVERT: B 255 GLN cc_start: 0.9304 (pt0) cc_final: 0.8805 (pm20) REVERT: B 301 ILE cc_start: 0.9654 (mt) cc_final: 0.9339 (mt) REVERT: B 303 TYR cc_start: 0.8064 (m-80) cc_final: 0.7664 (m-80) REVERT: B 313 MET cc_start: 0.9380 (tpt) cc_final: 0.9156 (tpp) REVERT: B 432 MET cc_start: 0.9299 (mtm) cc_final: 0.8757 (ptp) REVERT: B 531 GLN cc_start: 0.8887 (pm20) cc_final: 0.8234 (tm-30) REVERT: B 542 MET cc_start: 0.9238 (mmm) cc_final: 0.8843 (mmm) REVERT: B 615 MET cc_start: 0.8462 (pmm) cc_final: 0.8255 (pmm) REVERT: B 697 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8345 (mt-10) REVERT: B 698 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8559 (mt-10) REVERT: B 762 ASN cc_start: 0.9024 (m-40) cc_final: 0.8551 (m-40) REVERT: B 789 MET cc_start: 0.8913 (mmp) cc_final: 0.8599 (mmm) REVERT: B 809 MET cc_start: 0.9019 (mtp) cc_final: 0.8790 (mtp) REVERT: B 839 MET cc_start: 0.9118 (mtp) cc_final: 0.8737 (mtp) REVERT: B 846 ILE cc_start: 0.9773 (mt) cc_final: 0.9571 (mt) REVERT: B 895 ASP cc_start: 0.8350 (m-30) cc_final: 0.7865 (p0) REVERT: B 910 VAL cc_start: 0.9234 (t) cc_final: 0.8740 (p) REVERT: B 1032 SER cc_start: 0.9722 (m) cc_final: 0.9330 (p) REVERT: B 1072 MET cc_start: 0.7916 (ttm) cc_final: 0.7698 (ttm) REVERT: B 1082 MET cc_start: 0.9309 (tpp) cc_final: 0.8635 (tpp) REVERT: B 1111 MET cc_start: 0.9646 (mmp) cc_final: 0.9254 (mmp) REVERT: B 1208 MET cc_start: 0.9346 (mtm) cc_final: 0.9057 (mtm) REVERT: C 75 MET cc_start: 0.9284 (tpp) cc_final: 0.8979 (tpp) REVERT: C 163 ILE cc_start: 0.9634 (pt) cc_final: 0.9220 (mp) REVERT: D 66 ARG cc_start: 0.7305 (ttm170) cc_final: 0.7097 (ttm170) REVERT: D 70 PHE cc_start: 0.8084 (m-80) cc_final: 0.7848 (m-80) REVERT: D 156 ASP cc_start: 0.8156 (p0) cc_final: 0.7886 (p0) REVERT: D 190 GLU cc_start: 0.7118 (pt0) cc_final: 0.6644 (tm-30) REVERT: E 179 GLN cc_start: 0.8922 (mp10) cc_final: 0.8704 (mp10) REVERT: E 215 MET cc_start: 0.8765 (ppp) cc_final: 0.8444 (ppp) REVERT: F 89 GLU cc_start: 0.9412 (mt-10) cc_final: 0.8993 (mt-10) REVERT: F 124 GLU cc_start: 0.9072 (tp30) cc_final: 0.8675 (tp30) REVERT: G 1 MET cc_start: 0.9533 (mmm) cc_final: 0.8829 (tpt) REVERT: G 14 HIS cc_start: 0.8478 (t-90) cc_final: 0.7876 (t-90) REVERT: G 51 TYR cc_start: 0.7718 (t80) cc_final: 0.7483 (t80) REVERT: G 58 ARG cc_start: 0.9026 (ptp-110) cc_final: 0.7708 (ptp-110) REVERT: G 60 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8719 (mmt-90) REVERT: H 27 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8301 (mm-30) REVERT: H 40 LEU cc_start: 0.9650 (tp) cc_final: 0.9425 (tp) REVERT: H 103 LYS cc_start: 0.9319 (tptt) cc_final: 0.8958 (tptm) REVERT: H 123 MET cc_start: 0.9218 (tmm) cc_final: 0.8376 (tmm) REVERT: I 2 THR cc_start: 0.7252 (t) cc_final: 0.6792 (p) REVERT: I 13 MET cc_start: 0.7095 (ptt) cc_final: 0.6024 (ppp) REVERT: I 17 ARG cc_start: 0.8316 (ttt180) cc_final: 0.7422 (tpp-160) REVERT: I 27 PHE cc_start: 0.8477 (m-80) cc_final: 0.7862 (m-10) REVERT: I 36 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7968 (tm-30) REVERT: I 45 ARG cc_start: 0.8420 (ttt90) cc_final: 0.8117 (tpp80) REVERT: I 73 ARG cc_start: 0.8654 (tmt170) cc_final: 0.8397 (tmt170) REVERT: I 81 ARG cc_start: 0.8200 (mpt180) cc_final: 0.7980 (mmt-90) REVERT: I 87 GLN cc_start: 0.8486 (mt0) cc_final: 0.7727 (mt0) REVERT: I 94 ASP cc_start: 0.8749 (p0) cc_final: 0.8503 (t0) REVERT: I 97 MET cc_start: 0.8520 (mmm) cc_final: 0.7694 (mmt) REVERT: J 58 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8754 (mm-30) REVERT: K 6 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7846 (mmm-85) REVERT: K 42 LEU cc_start: 0.9459 (tp) cc_final: 0.9217 (tp) REVERT: K 49 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9045 (tm-30) REVERT: K 76 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8310 (tm-30) REVERT: K 106 GLU cc_start: 0.9021 (tp30) cc_final: 0.8755 (tp30) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.2120 time to fit residues: 163.2919 Evaluate side-chains 394 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 4 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 370 optimal weight: 9.9990 chunk 367 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 381 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 433 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN B1161 HIS ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 150 ASN E 61 GLN E 101 GLN G 153 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.065356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.044743 restraints weight = 148614.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.046089 restraints weight = 82203.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.046917 restraints weight = 55409.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.047538 restraints weight = 43158.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.047912 restraints weight = 36448.391| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 33702 Z= 0.296 Angle : 0.720 13.948 45889 Z= 0.365 Chirality : 0.045 0.245 5156 Planarity : 0.005 0.052 5604 Dihedral : 17.078 138.340 5256 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3833 helix: 1.34 (0.14), residues: 1330 sheet: -0.43 (0.20), residues: 615 loop : -0.50 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 45 TYR 0.024 0.002 TYR G 25 PHE 0.020 0.002 PHE A 655 TRP 0.019 0.002 TRP A 233 HIS 0.010 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.30 (33670) covalent geometry : angle 0.70439 / 0.36 (45844) hydrogen bonds : bond 0.04153 / 2.72 ( 1422) hydrogen bonds : angle 4.93900 / 3.53 ( 3933) metal coordination : bond 0.01328 / 0.90 ( 32) metal coordination : angle 4.77662 / 3.16 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7666 Ramachandran restraints generated. 3833 Oldfield, 0 Emsley, 3833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9396 (mmm) cc_final: 0.9070 (mmm) REVERT: A 222 LEU cc_start: 0.9695 (mt) cc_final: 0.9392 (mt) REVERT: A 444 PHE cc_start: 0.8970 (t80) cc_final: 0.8357 (t80) REVERT: A 487 MET cc_start: 0.9241 (mtm) cc_final: 0.8466 (ttm) REVERT: A 549 MET cc_start: 0.9573 (mmm) cc_final: 0.8960 (mmm) REVERT: A 676 MET cc_start: 0.9072 (mmt) cc_final: 0.8863 (mmp) REVERT: A 746 MET cc_start: 0.9323 (mtm) cc_final: 0.9109 (mtt) REVERT: A 748 MET cc_start: 0.8900 (mpp) cc_final: 0.8631 (mpp) REVERT: A 818 MET cc_start: 0.8989 (mtp) cc_final: 0.8722 (mtp) REVERT: A 849 MET cc_start: 0.8695 (ttp) cc_final: 0.8190 (ttp) REVERT: A 873 MET cc_start: 0.9335 (mmp) cc_final: 0.8920 (mmp) REVERT: A 1063 MET cc_start: 0.9228 (mmm) cc_final: 0.8826 (mmm) REVERT: A 1280 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7978 (mp0) REVERT: A 1284 MET cc_start: 0.8703 (ttm) cc_final: 0.8369 (ttt) REVERT: A 1373 ASP cc_start: 0.9182 (m-30) cc_final: 0.8866 (m-30) REVERT: A 1444 MET cc_start: 0.8386 (mmm) cc_final: 0.6991 (mtp) REVERT: B 101 MET cc_start: 0.9449 (mtp) cc_final: 0.9176 (mtp) REVERT: B 145 ARG cc_start: 0.8546 (mtp180) cc_final: 0.8142 (ttp80) REVERT: B 173 MET cc_start: 0.9264 (ttp) cc_final: 0.9008 (ttp) REVERT: B 199 MET cc_start: 0.8579 (mmp) cc_final: 0.8362 (mmp) REVERT: B 239 GLU cc_start: 0.9120 (pt0) cc_final: 0.8782 (pm20) REVERT: B 255 GLN cc_start: 0.9341 (pt0) cc_final: 0.8946 (pm20) REVERT: B 301 ILE cc_start: 0.9647 (mt) cc_final: 0.9382 (mt) REVERT: B 303 TYR cc_start: 0.8246 (m-80) cc_final: 0.7824 (m-80) REVERT: B 313 MET cc_start: 0.9402 (tpt) cc_final: 0.9177 (tpp) REVERT: B 432 MET cc_start: 0.9347 (mtm) cc_final: 0.8876 (ptm) REVERT: B 531 GLN cc_start: 0.8935 (pm20) cc_final: 0.8286 (tm-30) REVERT: B 542 MET cc_start: 0.9267 (mmm) cc_final: 0.9008 (mmm) REVERT: B 615 MET cc_start: 0.8548 (pmm) cc_final: 0.8251 (pmm) REVERT: B 618 ASP cc_start: 0.9234 (t70) cc_final: 0.7868 (t0) REVERT: B 621 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8809 (mp0) REVERT: B 697 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 698 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8524 (mt-10) REVERT: B 762 ASN cc_start: 0.9119 (m-40) cc_final: 0.8612 (m-40) REVERT: B 789 MET cc_start: 0.8924 (mmp) cc_final: 0.8588 (mmm) REVERT: B 809 MET cc_start: 0.9128 (mtp) cc_final: 0.8890 (mtp) REVERT: B 839 MET cc_start: 0.9218 (mtp) cc_final: 0.8802 (mtp) REVERT: B 842 ASN cc_start: 0.9494 (t0) cc_final: 0.9095 (t0) REVERT: B 845 SER cc_start: 0.9610 (t) cc_final: 0.9309 (p) REVERT: B 895 ASP cc_start: 0.8295 (m-30) cc_final: 0.7944 (p0) REVERT: B 1032 SER cc_start: 0.9747 (m) cc_final: 0.9391 (p) REVERT: B 1070 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8118 (tt0) REVERT: B 1082 MET cc_start: 0.9278 (tpp) cc_final: 0.8699 (tpp) REVERT: B 1111 MET cc_start: 0.9541 (mmp) cc_final: 0.8988 (mmp) REVERT: B 1152 MET cc_start: 0.9131 (mmm) cc_final: 0.8629 (tpt) REVERT: C 75 MET cc_start: 0.9275 (tpp) cc_final: 0.8984 (tpp) REVERT: D 6 SER cc_start: 0.8734 (t) cc_final: 0.8478 (m) REVERT: D 56 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7952 (ptm-80) REVERT: D 156 ASP cc_start: 0.8239 (p0) cc_final: 0.7960 (p0) REVERT: E 22 MET cc_start: 0.9355 (tmm) cc_final: 0.9105 (tmm) REVERT: E 179 GLN cc_start: 0.8972 (mp10) cc_final: 0.8745 (mp10) REVERT: E 215 MET cc_start: 0.8763 (ppp) cc_final: 0.8366 (ppp) REVERT: F 124 GLU cc_start: 0.9093 (tp30) cc_final: 0.8690 (tp30) REVERT: G 1 MET cc_start: 0.9538 (mmm) cc_final: 0.8841 (tpt) REVERT: G 14 HIS cc_start: 0.8515 (t-90) cc_final: 0.7951 (t-90) REVERT: G 51 TYR cc_start: 0.7718 (t80) cc_final: 0.7484 (t80) REVERT: G 58 ARG cc_start: 0.9025 (ptp-110) cc_final: 0.7703 (ptp-110) REVERT: G 60 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8735 (mmt-90) REVERT: H 26 ILE cc_start: 0.9533 (pt) cc_final: 0.9292 (pt) REVERT: H 40 LEU cc_start: 0.9675 (tp) cc_final: 0.9372 (tt) REVERT: H 105 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8039 (tm-30) REVERT: H 123 MET cc_start: 0.9210 (tmm) cc_final: 0.8394 (tmm) REVERT: H 129 TYR cc_start: 0.8961 (p90) cc_final: 0.8170 (p90) REVERT: I 2 THR cc_start: 0.7399 (t) cc_final: 0.7142 (p) REVERT: I 13 MET cc_start: 0.7233 (ptt) cc_final: 0.6045 (ppp) REVERT: I 17 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7396 (tpp-160) REVERT: I 27 PHE cc_start: 0.8480 (m-80) cc_final: 0.7947 (m-10) REVERT: I 34 TYR cc_start: 0.8010 (t80) cc_final: 0.7408 (t80) REVERT: I 36 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8142 (tm-30) REVERT: I 87 GLN cc_start: 0.8628 (mt0) cc_final: 0.7823 (mt0) REVERT: I 94 ASP cc_start: 0.8783 (p0) cc_final: 0.8490 (t0) REVERT: I 97 MET cc_start: 0.8587 (mmm) cc_final: 0.7778 (mmt) REVERT: J 42 LYS cc_start: 0.9391 (ptmm) cc_final: 0.9178 (ptpp) REVERT: J 49 MET cc_start: 0.9460 (tpp) cc_final: 0.9129 (tpp) REVERT: K 6 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7932 (mmm-85) REVERT: K 76 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8346 (tm-30) REVERT: K 106 GLU cc_start: 0.9047 (tp30) cc_final: 0.8792 (tp30) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2144 time to fit residues: 155.2428 Evaluate side-chains 367 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 38 optimal weight: 10.0000 chunk 169 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 228 optimal weight: 0.0030 chunk 226 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 385 optimal weight: 50.0000 chunk 208 optimal weight: 0.8980 chunk 230 optimal weight: 0.0870 chunk 134 optimal weight: 0.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 188 HIS E 61 GLN G 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.046931 restraints weight = 142708.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.048267 restraints weight = 78928.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.049147 restraints weight = 53366.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.049767 restraints weight = 41334.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.049982 restraints weight = 34926.609| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33702 Z= 0.116 Angle : 0.619 13.618 45889 Z= 0.315 Chirality : 0.044 0.235 5156 Planarity : 0.004 0.052 5604 Dihedral : 16.988 136.709 5256 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.62 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.77 % 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: 3833 helix: 1.42 (0.14), residues: 1331 sheet: -0.33 (0.21), residues: 614 loop : -0.42 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 63 TYR 0.023 0.001 TYR H 129 PHE 0.016 0.001 PHE I 86 TRP 0.016 0.001 TRP B 561 HIS 0.012 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (33670) covalent geometry : angle 0.60566 / 0.31 (45844) hydrogen bonds : bond 0.03523 / 2.29 ( 1422) hydrogen bonds : angle 4.64029 / 3.31 ( 3933) metal coordination : bond 0.00607 / 0.40 ( 32) metal coordination : angle 4.12127 / 2.66 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5701.31 seconds wall clock time: 99 minutes 34.25 seconds (5974.25 seconds total)