Starting phenix.real_space_refine on Sun Aug 9 09:39:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbl_54730/08_2026/9sbl_54730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbl_54730/08_2026/9sbl_54730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbl_54730/08_2026/9sbl_54730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbl_54730/08_2026/9sbl_54730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbl_54730/08_2026/9sbl_54730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbl_54730/08_2026/9sbl_54730.map" } resolution = 4.28 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 20449 2.51 5 N 5731 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32888 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: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 9142 Classifications: {'peptide': 1148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1098} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 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 67 108.371 68.894 95.255 1.00234.59 S ATOM 479 SG CYS A 70 107.613 65.474 93.789 1.00227.49 S ATOM 532 SG CYS A 77 105.208 68.214 93.205 1.00231.24 S ATOM 762 SG CYS A 107 82.632 74.269 135.788 1.00249.66 S ATOM 786 SG CYS A 110 84.242 70.974 136.333 1.00233.03 S ATOM 1091 SG CYS A 148 81.034 71.502 138.002 1.00252.01 S ATOM 1105 SG CYS A 167 84.019 73.609 139.221 1.00257.15 S ATOM 19507 SG CYS B1163 100.201 56.097 104.977 1.00217.25 S ATOM 19525 SG CYS B1166 98.137 59.325 104.872 1.00225.34 S ATOM 19650 SG CYS B1182 101.891 59.443 104.899 1.00216.79 S ATOM 19669 SG CYS B1185 100.051 58.384 108.055 1.00237.78 S ATOM 20657 SG CYS C 86 94.523 74.499 26.875 1.00266.00 S ATOM 20674 SG CYS C 88 96.986 76.679 28.454 1.00254.51 S ATOM 20707 SG CYS C 92 95.714 77.688 25.165 1.00249.72 S ATOM 20730 SG CYS C 95 93.459 77.975 28.168 1.00252.49 S ATOM 28315 SG CYS I 7 37.911 127.169 126.178 1.00408.92 S ATOM 28340 SG CYS I 10 41.563 126.219 126.093 1.00398.76 S ATOM 28506 SG CYS I 29 39.258 124.201 128.271 1.00453.16 S ATOM 28530 SG CYS I 32 39.885 127.779 129.276 1.00450.88 S ATOM 28857 SG CYS I 75 17.486 119.541 86.661 1.00488.17 S ATOM 28879 SG CYS I 78 17.746 123.232 85.780 1.00478.85 S ATOM 29095 SG CYS I 103 20.732 121.059 85.268 1.00465.46 S ATOM 29115 SG CYS I 106 19.638 121.758 88.818 1.00476.01 S ATOM 29217 SG CYS J 7 65.222 90.274 38.155 1.00198.47 S ATOM 29240 SG CYS J 10 65.355 88.390 34.803 1.00201.75 S ATOM 29520 SG CYS J 45 62.019 89.455 36.354 1.00193.08 S ATOM 29526 SG CYS J 46 64.433 91.951 34.758 1.00220.74 S ATOM 30649 SG CYS L 31 98.079 114.394 55.283 1.00424.53 S ATOM 30669 SG CYS L 34 99.114 116.059 52.123 1.00408.79 S ATOM 30773 SG CYS L 48 101.666 114.940 54.955 1.00395.78 S ATOM 30796 SG CYS L 51 99.367 118.017 55.307 1.00411.09 S Time building chain proxies: 6.73, per 1000 atoms: 0.20 Number of scatterers: 32888 At special positions: 0 Unit cell: (153.417, 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 6421 8.00 N 5731 7.00 C 20449 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: 2.94 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 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " 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 148 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " 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 B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " 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 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " 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: 7318 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 47 sheets defined 39.1% alpha, 20.1% beta 40 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 4.27 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 105 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.510A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.605A pdb=" N LYS A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.604A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.701A 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 removed outlier: 3.554A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.991A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.121A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.653A 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 removed outlier: 3.575A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.278A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 672 through 701 removed outlier: 4.480A pdb=" N ASN A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) 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: 3.705A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.837A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.110A 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 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.682A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 3.781A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 removed outlier: 3.505A pdb=" N SER A1145 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for '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 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.619A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.944A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.812A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.722A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.603A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.975A pdb=" N LEU B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.596A 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 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.568A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.657A 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: 3.964A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.541A 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: 3.782A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.579A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.677A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.899A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.742A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.714A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.866A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.543A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.544A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.681A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.516A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 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 removed outlier: 3.540A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.977A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.632A pdb=" N ALA D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) 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 27 removed outlier: 3.624A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.539A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 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 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 188 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 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.908A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 removed outlier: 4.034A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 Processing helix chain 'I' and resid 20 through 23 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.876A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.637A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.232A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 3.860A pdb=" N GLY A 82 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (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: 3.687A 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: 3.729A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.974A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.553A 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: 3.584A 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 589 through 590 removed outlier: 6.834A 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: 3.562A 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 removed outlier: 3.679A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.548A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1226 removed outlier: 4.304A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A1150 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.816A pdb=" N LYS G 5 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.279A 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: 3.800A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS G 5 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.721A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.721A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE B 166 " --> 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 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.136A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.076A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 547 removed outlier: 4.326A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.546A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 585 through 590 removed outlier: 7.070A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.871A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.871A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 removed outlier: 3.510A pdb=" N THR B 805 " --> pdb=" O GLY B1042 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.062A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 821 " --> pdb=" O TYR B1092 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.678A pdb=" N THR B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 removed outlier: 3.523A pdb=" N LYS B1174 " --> pdb=" O GLN B1179 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.662A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 18 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 230 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 7.436A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.533A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.858A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.524A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.615A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.645A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.701A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.111A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.544A pdb=" N PHE K 71 " --> pdb=" O PHE K 35 " (cutoff:3.500A) 1353 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 9.88 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10562 1.34 - 1.46: 6820 1.46 - 1.58: 15797 1.58 - 1.70: 187 1.70 - 1.82: 292 Bond restraints: 33658 Sorted by residual: bond pdb=" O5' ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.579 1.510 0.069 1.10e-02 8.26e+03 3.95e+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 3.95e+01 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.94e+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 3.93e+01 bond pdb=" C1' DC T 31 " pdb=" N1 DC T 31 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 ... (remaining 33653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 45586 3.24 - 6.48: 205 6.48 - 9.72: 37 9.72 - 12.96: 1 12.96 - 16.20: 2 Bond angle restraints: 45831 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 123.67 16.20 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 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" C THR A 709 " pdb=" CA THR A 709 " pdb=" CB THR A 709 " ideal model delta sigma weight residual 115.79 109.49 6.30 1.19e+00 7.06e-01 2.80e+01 angle pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " ideal model delta sigma weight residual 101.57 109.24 -7.67 1.54e+00 4.24e-01 2.49e+01 angle pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " pdb=" O3G ATP B1301 " ideal model delta sigma weight residual 104.48 109.46 -4.98 1.14e+00 7.76e-01 1.92e+01 ... (remaining 45826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 19720 35.17 - 70.34: 563 70.34 - 105.51: 47 105.51 - 140.68: 3 140.68 - 175.84: 4 Dihedral angle restraints: 20337 sinusoidal: 9042 harmonic: 11295 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 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLN A 68 " pdb=" C GLN A 68 " pdb=" N THR A 69 " pdb=" CA THR A 69 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" C4' DC T 39 " pdb=" C3' DC T 39 " pdb=" O3' DC T 39 " pdb=" P DA T 40 " ideal model delta sinusoidal sigma weight residual 220.00 44.16 175.84 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 20334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3601 0.037 - 0.075: 1041 0.075 - 0.112: 399 0.112 - 0.149: 107 0.149 - 0.186: 7 Chirality restraints: 5155 Sorted by residual: chirality pdb=" CB THR A 694 " pdb=" CA THR A 694 " pdb=" OG1 THR A 694 " pdb=" CG2 THR A 694 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C3' DT N 50 " pdb=" C4' DT N 50 " pdb=" O3' DT N 50 " pdb=" C2' DT N 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" C3' DG N 52 " pdb=" C4' DG N 52 " pdb=" O3' DG N 52 " pdb=" C2' DG N 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 5152 not shown) Planarity restraints: 5603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 173 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO D 174 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 75 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO I 76 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A1099 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.024 5.00e-02 4.00e+02 ... (remaining 5600 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 769 2.66 - 3.22: 32026 3.22 - 3.78: 54249 3.78 - 4.34: 72692 4.34 - 4.90: 113696 Nonbonded interactions: 273432 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1801 " model vdw 2.098 2.170 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 2.110 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1801 " model vdw 2.123 2.170 nonbonded pdb=" OG SER E 157 " pdb=" OE1 GLU E 160 " model vdw 2.141 3.040 nonbonded pdb=" OG SER B1056 " pdb=" OG SER B1066 " model vdw 2.157 3.040 ... (remaining 273427 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: 2.830 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 39.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 33690 Z= 0.258 Angle : 0.642 16.204 45876 Z= 0.420 Chirality : 0.043 0.186 5155 Planarity : 0.004 0.046 5603 Dihedral : 15.398 175.844 13019 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % 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: 0.71 (0.14), residues: 3833 helix: 1.82 (0.15), residues: 1279 sheet: 0.16 (0.22), residues: 543 loop : -0.29 (0.15), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 591 TYR 0.018 0.001 TYR A1349 PHE 0.025 0.001 PHE A 444 TRP 0.025 0.002 TRP B 466 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.26 (33658) covalent geometry : angle 0.63434 / 0.42 (45831) hydrogen bonds : bond 0.20184 / 13.58 ( 1412) hydrogen bonds : angle 7.29827 / 5.12 ( 3928) metal coordination : bond 0.01745 / 1.27 ( 32) metal coordination : angle 3.19257 / 2.11 ( 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 727 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 726 time to evaluate : 1.250 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: 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 353 ILE cc_start: 0.9587 (pt) cc_final: 0.9336 (mp) REVERT: A 453 MET cc_start: 0.9456 (mpp) cc_final: 0.9016 (mpp) REVERT: A 455 MET cc_start: 0.8703 (ttt) cc_final: 0.8141 (ttt) REVERT: A 487 MET cc_start: 0.8850 (mtp) cc_final: 0.8547 (mtp) REVERT: A 605 MET cc_start: 0.9273 (tpp) cc_final: 0.8864 (tpp) REVERT: A 606 LEU cc_start: 0.9634 (tp) cc_final: 0.9310 (tp) REVERT: A 676 MET cc_start: 0.9037 (mmm) cc_final: 0.8797 (mmm) REVERT: A 714 PHE cc_start: 0.9427 (t80) cc_final: 0.9218 (t80) REVERT: A 731 ARG cc_start: 0.9602 (mmt180) cc_final: 0.9285 (mmp80) REVERT: A 734 GLU cc_start: 0.9425 (tt0) cc_final: 0.8774 (tm-30) REVERT: A 746 MET cc_start: 0.9435 (mtm) cc_final: 0.9071 (mtm) REVERT: A 748 MET cc_start: 0.9490 (mtm) cc_final: 0.8836 (mtp) REVERT: A 842 VAL cc_start: 0.9731 (t) cc_final: 0.9518 (p) REVERT: A 846 GLU cc_start: 0.9064 (pt0) cc_final: 0.8804 (pt0) REVERT: A 874 ASP cc_start: 0.9366 (t0) cc_final: 0.8280 (p0) REVERT: A 935 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: A 956 LEU cc_start: 0.9405 (mt) cc_final: 0.9168 (mp) REVERT: A 1336 MET cc_start: 0.9442 (ttt) cc_final: 0.9202 (tmm) REVERT: A 1337 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8773 (pt0) REVERT: A 1349 TYR cc_start: 0.9459 (t80) cc_final: 0.9211 (t80) REVERT: A 1393 ASN cc_start: 0.9109 (p0) cc_final: 0.8662 (t0) REVERT: A 1417 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 224 GLN cc_start: 0.9604 (mt0) cc_final: 0.9354 (mp10) REVERT: B 259 TYR cc_start: 0.8748 (m-80) cc_final: 0.8035 (m-80) REVERT: B 320 ASP cc_start: 0.9489 (m-30) cc_final: 0.9279 (m-30) REVERT: B 381 MET cc_start: 0.9654 (mtp) cc_final: 0.9391 (mtp) REVERT: B 404 LYS cc_start: 0.9713 (mttm) cc_final: 0.9454 (mtmm) REVERT: B 488 TYR cc_start: 0.9043 (t80) cc_final: 0.8642 (t80) REVERT: B 514 LEU cc_start: 0.9377 (tp) cc_final: 0.8657 (tp) REVERT: B 526 GLU cc_start: 0.9222 (tt0) cc_final: 0.8996 (tp30) REVERT: B 615 MET cc_start: 0.8691 (mtm) cc_final: 0.8446 (mpp) REVERT: B 621 GLU cc_start: 0.9315 (mp0) cc_final: 0.9060 (mp0) REVERT: B 625 LYS cc_start: 0.9710 (mttt) cc_final: 0.9478 (mtpp) REVERT: B 643 ASP cc_start: 0.8769 (t0) cc_final: 0.8361 (p0) REVERT: B 698 GLU cc_start: 0.9536 (tt0) cc_final: 0.9149 (tm-30) REVERT: B 747 MET cc_start: 0.9466 (mmm) cc_final: 0.8603 (mmm) REVERT: B 762 ASN cc_start: 0.9010 (m-40) cc_final: 0.8113 (m-40) REVERT: B 763 GLN cc_start: 0.9331 (tt0) cc_final: 0.9108 (pt0) REVERT: B 775 LYS cc_start: 0.9492 (mtmt) cc_final: 0.9064 (mtmm) REVERT: B 778 MET cc_start: 0.9421 (ttm) cc_final: 0.8969 (ttp) REVERT: B 789 MET cc_start: 0.8564 (mmm) cc_final: 0.8051 (mmm) REVERT: B 821 GLN cc_start: 0.8892 (mp10) cc_final: 0.8636 (mp10) REVERT: B 825 VAL cc_start: 0.9493 (t) cc_final: 0.9170 (m) REVERT: B 846 ILE cc_start: 0.9767 (mt) cc_final: 0.9393 (mm) REVERT: B 992 ILE cc_start: 0.9323 (tt) cc_final: 0.9096 (tt) REVERT: B 995 ARG cc_start: 0.9409 (mtm180) cc_final: 0.9207 (mtm-85) REVERT: B 999 MET cc_start: 0.9319 (mmt) cc_final: 0.8944 (mmt) REVERT: B 1028 GLU cc_start: 0.9544 (tt0) cc_final: 0.9084 (tm-30) REVERT: B 1101 ASP cc_start: 0.9775 (m-30) cc_final: 0.9521 (m-30) REVERT: B 1111 MET cc_start: 0.9108 (mmm) cc_final: 0.8798 (mmm) REVERT: B 1120 GLU cc_start: 0.9012 (pm20) cc_final: 0.8791 (pm20) REVERT: C 26 ASP cc_start: 0.8990 (p0) cc_final: 0.8677 (p0) REVERT: C 29 MET cc_start: 0.9467 (ttm) cc_final: 0.8990 (mtt) REVERT: C 38 ILE cc_start: 0.9676 (mt) cc_final: 0.9441 (tt) REVERT: C 66 ARG cc_start: 0.9152 (ttm-80) cc_final: 0.8829 (ttm-80) REVERT: C 152 GLU cc_start: 0.8864 (tt0) cc_final: 0.8646 (tp30) REVERT: C 166 GLU cc_start: 0.9013 (tt0) cc_final: 0.8685 (tp30) REVERT: C 230 MET cc_start: 0.9782 (mtt) cc_final: 0.9044 (mmp) REVERT: D 50 LEU cc_start: 0.8553 (mt) cc_final: 0.8293 (mm) REVERT: D 119 ARG cc_start: 0.5181 (mpt180) cc_final: 0.4771 (mmp80) REVERT: D 120 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7539 (pp20) REVERT: D 207 LEU cc_start: 0.7958 (tp) cc_final: 0.7520 (mt) REVERT: D 209 ARG cc_start: 0.8867 (tmt170) cc_final: 0.8513 (tmt170) REVERT: E 32 GLN cc_start: 0.9534 (tt0) cc_final: 0.9001 (tp-100) REVERT: E 57 MET cc_start: 0.9430 (mtm) cc_final: 0.8922 (mtp) REVERT: E 215 MET cc_start: 0.9145 (ptt) cc_final: 0.8619 (ppp) REVERT: F 110 ASP cc_start: 0.9509 (m-30) cc_final: 0.9031 (t0) REVERT: F 111 LEU cc_start: 0.9654 (mt) cc_final: 0.9397 (mm) REVERT: F 114 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8522 (tm-30) REVERT: F 119 ARG cc_start: 0.9590 (tpp80) cc_final: 0.9219 (tpp80) REVERT: F 123 LYS cc_start: 0.9600 (tttm) cc_final: 0.9347 (tttt) REVERT: F 124 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9448 (mm-30) REVERT: G 51 TYR cc_start: 0.9042 (t80) cc_final: 0.8523 (t80) REVERT: G 60 ARG cc_start: 0.9336 (ttp80) cc_final: 0.8875 (ttp80) REVERT: G 71 ASN cc_start: 0.7950 (t0) cc_final: 0.7602 (p0) REVERT: G 73 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8468 (mtpt) REVERT: G 82 PHE cc_start: 0.7312 (m-80) cc_final: 0.6691 (m-80) REVERT: G 119 LEU cc_start: 0.5283 (mp) cc_final: 0.5065 (tp) REVERT: H 14 GLU cc_start: 0.9139 (tt0) cc_final: 0.8781 (tm-30) REVERT: H 27 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9340 (mp0) REVERT: H 42 ILE cc_start: 0.9724 (mm) cc_final: 0.9516 (mm) REVERT: H 123 MET cc_start: 0.9632 (ttt) cc_final: 0.9169 (tmm) REVERT: I 3 THR cc_start: 0.9446 (m) cc_final: 0.8910 (p) REVERT: I 9 ASP cc_start: 0.8605 (t70) cc_final: 0.8391 (t70) REVERT: I 58 VAL cc_start: 0.8874 (p) cc_final: 0.8539 (t) REVERT: I 62 ILE cc_start: 0.8776 (mm) cc_final: 0.8549 (mm) REVERT: I 68 LEU cc_start: 0.9243 (mt) cc_final: 0.8784 (pp) REVERT: I 92 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7935 (tpp80) REVERT: I 100 PHE cc_start: 0.7366 (m-80) cc_final: 0.7163 (m-10) REVERT: I 110 PHE cc_start: 0.1573 (m-80) cc_final: 0.1130 (m-80) REVERT: J 22 LEU cc_start: 0.9730 (tt) cc_final: 0.9480 (tt) REVERT: J 32 GLU cc_start: 0.9273 (mp0) cc_final: 0.9060 (mm-30) REVERT: J 49 MET cc_start: 0.9609 (tpp) cc_final: 0.8898 (mmm) REVERT: J 57 ILE cc_start: 0.9822 (tp) cc_final: 0.9589 (mm) REVERT: J 58 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9194 (mp0) REVERT: K 8 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8333 (mt-10) REVERT: K 19 LEU cc_start: 0.9368 (mt) cc_final: 0.9131 (mp) REVERT: K 36 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8515 (mp0) REVERT: K 64 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8705 (mt-10) REVERT: K 75 ILE cc_start: 0.9624 (mt) cc_final: 0.9410 (mp) REVERT: K 91 CYS cc_start: 0.9817 (m) cc_final: 0.9388 (p) REVERT: L 47 ARG cc_start: 0.8327 (ptm160) cc_final: 0.7524 (ttt-90) REVERT: L 67 PHE cc_start: 0.9067 (m-80) cc_final: 0.8742 (m-80) outliers start: 1 outliers final: 0 residues processed: 727 average time/residue: 0.2318 time to fit residues: 267.6361 Evaluate side-chains 475 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 510 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN B 433 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 HIS ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN K 89 ASN ** L 53 HIS ** 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 = 0.3132 r_free = 0.3132 target = 0.059884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.041415 restraints weight = 171849.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.042610 restraints weight = 99169.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.043458 restraints weight = 68319.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.044054 restraints weight = 52915.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.044386 restraints weight = 44301.321| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33690 Z= 0.255 Angle : 0.727 17.484 45876 Z= 0.375 Chirality : 0.047 0.347 5155 Planarity : 0.005 0.071 5603 Dihedral : 17.558 179.396 5255 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % 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: 0.34 (0.14), residues: 3833 helix: 1.53 (0.14), residues: 1304 sheet: -0.26 (0.21), residues: 576 loop : -0.48 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 144 TYR 0.024 0.002 TYR D 147 PHE 0.048 0.002 PHE A1402 TRP 0.023 0.002 TRP B 466 HIS 0.010 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (33658) covalent geometry : angle 0.70566 / 0.37 (45831) hydrogen bonds : bond 0.05291 / 3.54 ( 1412) hydrogen bonds : angle 5.82014 / 4.07 ( 3928) metal coordination : bond 0.01421 / 0.85 ( 32) metal coordination : angle 5.65889 / 3.65 ( 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 542 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 540 time to evaluate : 1.287 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: 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: 0.8845 (mtm) cc_final: 0.8478 (mtt) REVERT: A 341 MET cc_start: 0.9389 (mmm) cc_final: 0.8993 (mmm) REVERT: A 453 MET cc_start: 0.9304 (mpp) cc_final: 0.8947 (mpp) REVERT: A 455 MET cc_start: 0.8956 (ttt) cc_final: 0.8699 (ttt) REVERT: A 487 MET cc_start: 0.8875 (mtp) cc_final: 0.8216 (mtp) REVERT: A 510 GLN cc_start: 0.9198 (mm110) cc_final: 0.8914 (mp10) REVERT: A 511 ILE cc_start: 0.9608 (mm) cc_final: 0.9294 (mm) REVERT: A 605 MET cc_start: 0.8941 (tpp) cc_final: 0.8507 (tpp) REVERT: A 606 LEU cc_start: 0.9603 (tp) cc_final: 0.9293 (tp) REVERT: A 676 MET cc_start: 0.8829 (mmm) cc_final: 0.8514 (mmm) REVERT: A 731 ARG cc_start: 0.9451 (mmt180) cc_final: 0.9209 (mmp80) REVERT: A 748 MET cc_start: 0.9458 (mtm) cc_final: 0.8918 (mtp) REVERT: A 761 MET cc_start: 0.9462 (mtp) cc_final: 0.9221 (mpp) REVERT: A 838 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8962 (tm-30) REVERT: A 849 MET cc_start: 0.8785 (tmm) cc_final: 0.8421 (tmm) REVERT: A 873 MET cc_start: 0.9377 (mmp) cc_final: 0.9019 (mmm) REVERT: A 874 ASP cc_start: 0.9314 (t0) cc_final: 0.8438 (p0) REVERT: A 932 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9152 (mm-30) REVERT: A 956 LEU cc_start: 0.9572 (mt) cc_final: 0.9297 (mp) REVERT: A 1267 MET cc_start: 0.8943 (mmm) cc_final: 0.8726 (mmm) REVERT: A 1337 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8698 (pt0) REVERT: A 1393 ASN cc_start: 0.9020 (p0) cc_final: 0.8581 (t0) REVERT: A 1404 GLU cc_start: 0.8684 (mt-10) cc_final: 0.7961 (mm-30) REVERT: A 1417 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8505 (mt-10) REVERT: B 224 GLN cc_start: 0.9577 (mt0) cc_final: 0.9366 (mp10) REVERT: B 282 ILE cc_start: 0.9631 (pt) cc_final: 0.9391 (mm) REVERT: B 381 MET cc_start: 0.9521 (mtp) cc_final: 0.9191 (mtp) REVERT: B 488 TYR cc_start: 0.9079 (t80) cc_final: 0.8841 (t80) REVERT: B 621 GLU cc_start: 0.9219 (mp0) cc_final: 0.9011 (mp0) REVERT: B 625 LYS cc_start: 0.9631 (mttt) cc_final: 0.9426 (mtpp) REVERT: B 643 ASP cc_start: 0.8380 (t0) cc_final: 0.8126 (p0) REVERT: B 698 GLU cc_start: 0.9382 (tt0) cc_final: 0.9133 (tm-30) REVERT: B 747 MET cc_start: 0.9399 (mmm) cc_final: 0.8746 (mmm) REVERT: B 762 ASN cc_start: 0.9023 (m-40) cc_final: 0.8284 (m-40) REVERT: B 775 LYS cc_start: 0.9522 (mtmt) cc_final: 0.9139 (mtmm) REVERT: B 778 MET cc_start: 0.9341 (ttm) cc_final: 0.9102 (ttp) REVERT: B 789 MET cc_start: 0.8457 (mmm) cc_final: 0.8011 (mmm) REVERT: B 821 GLN cc_start: 0.8866 (mp10) cc_final: 0.8374 (mp10) REVERT: B 841 MET cc_start: 0.8969 (ttm) cc_final: 0.8583 (ttm) REVERT: B 846 ILE cc_start: 0.9737 (mt) cc_final: 0.9305 (mm) REVERT: B 992 ILE cc_start: 0.9359 (tt) cc_final: 0.8552 (pt) REVERT: B 999 MET cc_start: 0.9037 (mmt) cc_final: 0.8770 (mmt) REVERT: B 1028 GLU cc_start: 0.9579 (tt0) cc_final: 0.8901 (tm-30) REVERT: B 1138 MET cc_start: 0.9415 (mmp) cc_final: 0.9131 (mmm) REVERT: B 1202 LEU cc_start: 0.9728 (tp) cc_final: 0.9490 (tp) REVERT: B 1206 GLU cc_start: 0.9647 (mt-10) cc_final: 0.9402 (mt-10) REVERT: B 1210 MET cc_start: 0.9476 (tpp) cc_final: 0.9118 (tpp) REVERT: C 26 ASP cc_start: 0.9062 (p0) cc_final: 0.8739 (p0) REVERT: C 29 MET cc_start: 0.9411 (ttm) cc_final: 0.9012 (mtt) REVERT: C 37 MET cc_start: 0.9471 (mtp) cc_final: 0.9025 (mtp) REVERT: C 166 GLU cc_start: 0.8907 (tt0) cc_final: 0.8587 (tp30) REVERT: D 50 LEU cc_start: 0.7687 (mt) cc_final: 0.7467 (mt) REVERT: D 119 ARG cc_start: 0.5225 (mpt180) cc_final: 0.4773 (mmp80) REVERT: D 120 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7580 (pp20) REVERT: E 32 GLN cc_start: 0.9266 (tt0) cc_final: 0.8814 (tp-100) REVERT: E 57 MET cc_start: 0.9258 (mtm) cc_final: 0.8946 (mtp) REVERT: E 58 MET cc_start: 0.8986 (mmm) cc_final: 0.8584 (mmm) REVERT: E 82 PHE cc_start: 0.9278 (m-10) cc_final: 0.9051 (m-80) REVERT: E 215 MET cc_start: 0.8934 (ptt) cc_final: 0.8625 (ppp) REVERT: F 99 LEU cc_start: 0.9676 (tp) cc_final: 0.9344 (tp) REVERT: F 103 MET cc_start: 0.9588 (mmp) cc_final: 0.9246 (mmm) REVERT: F 110 ASP cc_start: 0.9431 (m-30) cc_final: 0.9227 (t0) REVERT: F 119 ARG cc_start: 0.9563 (tpp80) cc_final: 0.9295 (tpp80) REVERT: F 124 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9107 (mm-30) REVERT: G 3 PHE cc_start: 0.9332 (m-80) cc_final: 0.8893 (m-80) REVERT: G 9 LEU cc_start: 0.8379 (tp) cc_final: 0.8094 (tt) REVERT: G 57 GLN cc_start: 0.4761 (mp10) cc_final: 0.4523 (mp10) REVERT: G 60 ARG cc_start: 0.9520 (ttp80) cc_final: 0.8837 (ttp80) REVERT: G 82 PHE cc_start: 0.6706 (m-80) cc_final: 0.6456 (m-80) REVERT: G 171 ILE cc_start: 0.5189 (mp) cc_final: 0.4964 (mp) REVERT: H 22 LYS cc_start: 0.9481 (mttp) cc_final: 0.9136 (mmmm) REVERT: H 43 ASN cc_start: 0.9825 (t0) cc_final: 0.9600 (t0) REVERT: H 45 GLU cc_start: 0.8393 (mp0) cc_final: 0.7706 (mp0) REVERT: H 123 MET cc_start: 0.9350 (ttt) cc_final: 0.9085 (tmm) REVERT: H 141 TYR cc_start: 0.9323 (m-80) cc_final: 0.8911 (m-80) REVERT: I 3 THR cc_start: 0.9408 (m) cc_final: 0.9190 (p) REVERT: I 68 LEU cc_start: 0.9326 (mt) cc_final: 0.8898 (pt) REVERT: I 95 THR cc_start: 0.8409 (m) cc_final: 0.7839 (m) REVERT: I 110 PHE cc_start: 0.2354 (m-80) cc_final: 0.1976 (m-10) REVERT: J 21 TYR cc_start: 0.9402 (t80) cc_final: 0.9067 (t80) REVERT: J 49 MET cc_start: 0.9456 (tpp) cc_final: 0.8689 (mmm) REVERT: J 57 ILE cc_start: 0.9710 (tp) cc_final: 0.9402 (pt) REVERT: K 52 ASN cc_start: 0.9405 (m110) cc_final: 0.9065 (m110) REVERT: K 91 CYS cc_start: 0.9694 (m) cc_final: 0.9302 (p) REVERT: L 30 ILE cc_start: 0.8801 (mm) cc_final: 0.8378 (tp) REVERT: L 47 ARG cc_start: 0.8874 (ptm160) cc_final: 0.7703 (ttt-90) REVERT: L 54 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8109 (mtp85) REVERT: L 56 LEU cc_start: 0.8612 (mt) cc_final: 0.8396 (mt) REVERT: L 57 LEU cc_start: 0.8750 (mp) cc_final: 0.8550 (mp) REVERT: L 66 GLN cc_start: 0.9200 (pp30) cc_final: 0.8845 (pp30) REVERT: L 67 PHE cc_start: 0.9038 (m-80) cc_final: 0.8777 (m-80) outliers start: 2 outliers final: 1 residues processed: 542 average time/residue: 0.2204 time to fit residues: 195.5058 Evaluate side-chains 427 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 236 optimal weight: 4.9990 chunk 386 optimal weight: 30.0000 chunk 289 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 302 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 167 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 108 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.041730 restraints weight = 170343.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.042988 restraints weight = 97813.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.043851 restraints weight = 67290.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.044400 restraints weight = 51984.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.044826 restraints weight = 43737.500| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33690 Z= 0.187 Angle : 0.652 12.354 45876 Z= 0.338 Chirality : 0.045 0.361 5155 Planarity : 0.004 0.070 5603 Dihedral : 17.529 178.855 5255 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % 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: 0.27 (0.14), residues: 3833 helix: 1.48 (0.14), residues: 1312 sheet: -0.37 (0.21), residues: 573 loop : -0.51 (0.15), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 75 TYR 0.025 0.001 TYR G 167 PHE 0.030 0.002 PHE I 4 TRP 0.023 0.001 TRP B 466 HIS 0.007 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (33658) covalent geometry : angle 0.63522 / 0.34 (45831) hydrogen bonds : bond 0.04424 / 2.95 ( 1412) hydrogen bonds : angle 5.41801 / 3.78 ( 3928) metal coordination : bond 0.00837 / 0.56 ( 32) metal coordination : angle 4.76797 / 3.02 ( 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 541 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 538 time to evaluate : 1.434 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: 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: 0.8781 (mtm) cc_final: 0.8471 (mtt) REVERT: A 341 MET cc_start: 0.9321 (mmm) cc_final: 0.9059 (mmm) REVERT: A 453 MET cc_start: 0.9136 (mpp) cc_final: 0.8852 (mpp) REVERT: A 455 MET cc_start: 0.9123 (ttt) cc_final: 0.8194 (ttt) REVERT: A 487 MET cc_start: 0.8635 (mtp) cc_final: 0.8279 (mtp) REVERT: A 605 MET cc_start: 0.8941 (tpp) cc_final: 0.8498 (tpp) REVERT: A 606 LEU cc_start: 0.9621 (tp) cc_final: 0.9312 (tp) REVERT: A 676 MET cc_start: 0.8884 (mmm) cc_final: 0.8557 (mmm) REVERT: A 731 ARG cc_start: 0.9420 (mmt180) cc_final: 0.9159 (mmp80) REVERT: A 748 MET cc_start: 0.9477 (mtm) cc_final: 0.8974 (mpp) REVERT: A 761 MET cc_start: 0.9434 (mtp) cc_final: 0.9192 (mpp) REVERT: A 838 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8813 (tm-30) REVERT: A 873 MET cc_start: 0.9357 (mmp) cc_final: 0.9037 (mmm) REVERT: A 874 ASP cc_start: 0.9271 (t0) cc_final: 0.8337 (p0) REVERT: A 932 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9153 (mm-30) REVERT: A 956 LEU cc_start: 0.9563 (mt) cc_final: 0.9306 (mp) REVERT: A 997 LEU cc_start: 0.9256 (mp) cc_final: 0.8612 (mt) REVERT: A 1317 MET cc_start: 0.9519 (ptp) cc_final: 0.9012 (ptp) REVERT: A 1337 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8653 (pt0) REVERT: A 1368 MET cc_start: 0.8838 (ptp) cc_final: 0.8510 (ptm) REVERT: A 1373 ASP cc_start: 0.9284 (m-30) cc_final: 0.8876 (m-30) REVERT: A 1378 GLN cc_start: 0.9543 (pm20) cc_final: 0.9301 (pm20) REVERT: A 1393 ASN cc_start: 0.9024 (p0) cc_final: 0.8593 (t0) REVERT: A 1404 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7994 (mm-30) REVERT: A 1417 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 1433 MET cc_start: 0.7773 (tpp) cc_final: 0.7485 (tpp) REVERT: B 224 GLN cc_start: 0.9586 (mt0) cc_final: 0.9370 (mp10) REVERT: B 310 MET cc_start: 0.9480 (mtp) cc_final: 0.9259 (mtp) REVERT: B 381 MET cc_start: 0.9486 (mtp) cc_final: 0.9136 (mtp) REVERT: B 488 TYR cc_start: 0.9083 (t80) cc_final: 0.8791 (t80) REVERT: B 521 LEU cc_start: 0.9719 (mt) cc_final: 0.9454 (mt) REVERT: B 526 GLU cc_start: 0.7643 (tp30) cc_final: 0.7156 (tp30) REVERT: B 624 LEU cc_start: 0.9495 (tp) cc_final: 0.8540 (tp) REVERT: B 625 LYS cc_start: 0.9570 (mttt) cc_final: 0.9368 (mtpp) REVERT: B 643 ASP cc_start: 0.8341 (t0) cc_final: 0.8097 (p0) REVERT: B 698 GLU cc_start: 0.9377 (tt0) cc_final: 0.9131 (tm-30) REVERT: B 747 MET cc_start: 0.9396 (mmm) cc_final: 0.8827 (mmm) REVERT: B 762 ASN cc_start: 0.9016 (m-40) cc_final: 0.8195 (m-40) REVERT: B 775 LYS cc_start: 0.9363 (mtmt) cc_final: 0.9032 (mtmm) REVERT: B 778 MET cc_start: 0.9294 (ttm) cc_final: 0.9061 (ttp) REVERT: B 789 MET cc_start: 0.8361 (mmm) cc_final: 0.7953 (mmm) REVERT: B 821 GLN cc_start: 0.8799 (mp10) cc_final: 0.8334 (mp10) REVERT: B 839 MET cc_start: 0.9199 (ptp) cc_final: 0.8965 (ptp) REVERT: B 841 MET cc_start: 0.9009 (ttm) cc_final: 0.8569 (ttm) REVERT: B 846 ILE cc_start: 0.9751 (mt) cc_final: 0.9314 (mm) REVERT: B 999 MET cc_start: 0.9029 (mmt) cc_final: 0.8732 (mmt) REVERT: B 1028 GLU cc_start: 0.9592 (tt0) cc_final: 0.8870 (tm-30) REVERT: B 1085 ILE cc_start: 0.9779 (mm) cc_final: 0.9574 (pt) REVERT: B 1098 MET cc_start: 0.9170 (mtm) cc_final: 0.8960 (mtm) REVERT: B 1117 GLN cc_start: 0.9362 (mt0) cc_final: 0.9142 (mm-40) REVERT: B 1132 GLU cc_start: 0.8604 (pm20) cc_final: 0.8396 (pp20) REVERT: B 1138 MET cc_start: 0.9348 (mmp) cc_final: 0.9118 (mmm) REVERT: B 1202 LEU cc_start: 0.9741 (tp) cc_final: 0.9513 (tp) REVERT: B 1203 LEU cc_start: 0.9862 (tt) cc_final: 0.9627 (tt) REVERT: B 1206 GLU cc_start: 0.9657 (mt-10) cc_final: 0.9399 (mt-10) REVERT: B 1207 LEU cc_start: 0.9901 (mm) cc_final: 0.9555 (tp) REVERT: B 1208 MET cc_start: 0.9485 (mtt) cc_final: 0.9229 (mtp) REVERT: C 26 ASP cc_start: 0.9019 (p0) cc_final: 0.8691 (p0) REVERT: C 29 MET cc_start: 0.9415 (ttm) cc_final: 0.9017 (mtt) REVERT: C 37 MET cc_start: 0.9376 (mtp) cc_final: 0.8947 (mtp) REVERT: C 166 GLU cc_start: 0.8853 (tt0) cc_final: 0.8510 (tp30) REVERT: D 119 ARG cc_start: 0.5145 (mpt180) cc_final: 0.4909 (mmp80) REVERT: E 32 GLN cc_start: 0.9291 (tt0) cc_final: 0.8855 (tp-100) REVERT: E 57 MET cc_start: 0.9323 (mtm) cc_final: 0.9095 (mtp) REVERT: E 58 MET cc_start: 0.8940 (mmm) cc_final: 0.8528 (mmm) REVERT: E 172 GLU cc_start: 0.9138 (pm20) cc_final: 0.8909 (pp20) REVERT: E 215 MET cc_start: 0.8957 (ptt) cc_final: 0.8619 (ppp) REVERT: F 88 TYR cc_start: 0.9608 (m-80) cc_final: 0.9365 (m-80) REVERT: F 103 MET cc_start: 0.9605 (mmp) cc_final: 0.9153 (mmm) REVERT: F 110 ASP cc_start: 0.9405 (m-30) cc_final: 0.9186 (t0) REVERT: F 119 ARG cc_start: 0.9622 (tpp80) cc_final: 0.9407 (mmm-85) REVERT: F 122 MET cc_start: 0.9678 (mtm) cc_final: 0.9153 (mtp) REVERT: F 124 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9029 (mm-30) REVERT: G 3 PHE cc_start: 0.9248 (m-80) cc_final: 0.8776 (m-80) REVERT: G 9 LEU cc_start: 0.8338 (tp) cc_final: 0.8033 (tt) REVERT: G 60 ARG cc_start: 0.9495 (ttp80) cc_final: 0.8868 (ttp80) REVERT: G 119 LEU cc_start: 0.5193 (mp) cc_final: 0.4897 (tp) REVERT: H 22 LYS cc_start: 0.9472 (mttp) cc_final: 0.9123 (mmmm) REVERT: H 45 GLU cc_start: 0.8425 (mp0) cc_final: 0.7739 (mp0) REVERT: H 103 LYS cc_start: 0.9623 (tppt) cc_final: 0.9379 (tppt) REVERT: I 1 MET cc_start: 0.7904 (ptt) cc_final: 0.7653 (ptt) REVERT: I 3 THR cc_start: 0.9411 (m) cc_final: 0.9086 (p) REVERT: I 5 ARG cc_start: 0.8756 (mmt90) cc_final: 0.8510 (mmt90) REVERT: I 9 ASP cc_start: 0.8695 (t70) cc_final: 0.8458 (t70) REVERT: I 45 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.8107 (ttt-90) REVERT: I 55 THR cc_start: 0.8397 (m) cc_final: 0.7929 (m) REVERT: I 68 LEU cc_start: 0.9368 (mt) cc_final: 0.8944 (pt) REVERT: I 97 MET cc_start: 0.8232 (ttp) cc_final: 0.8023 (mmm) REVERT: I 110 PHE cc_start: 0.3311 (m-80) cc_final: 0.2389 (m-80) REVERT: J 21 TYR cc_start: 0.9494 (t80) cc_final: 0.9267 (t80) REVERT: J 27 GLU cc_start: 0.8343 (pp20) cc_final: 0.8127 (pp20) REVERT: J 49 MET cc_start: 0.9357 (tpp) cc_final: 0.8822 (mmm) REVERT: K 52 ASN cc_start: 0.9301 (m110) cc_final: 0.8979 (m110) REVERT: L 30 ILE cc_start: 0.8776 (mm) cc_final: 0.8410 (tp) REVERT: L 47 ARG cc_start: 0.8814 (ptm160) cc_final: 0.7768 (mtp180) REVERT: L 56 LEU cc_start: 0.8653 (mt) cc_final: 0.8433 (mt) REVERT: L 63 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8488 (ptm-80) REVERT: L 66 GLN cc_start: 0.9248 (pp30) cc_final: 0.9026 (pp30) outliers start: 3 outliers final: 0 residues processed: 541 average time/residue: 0.2155 time to fit residues: 190.5052 Evaluate side-chains 421 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 53 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 372 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 387 optimal weight: 40.0000 chunk 18 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 HIS B1179 GLN D 173 HIS E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** 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 = 0.3105 r_free = 0.3105 target = 0.058754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.040389 restraints weight = 175708.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.041609 restraints weight = 102210.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.042415 restraints weight = 70612.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.042913 restraints weight = 54902.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.043315 restraints weight = 46798.031| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 33690 Z= 0.297 Angle : 0.740 12.132 45876 Z= 0.378 Chirality : 0.045 0.366 5155 Planarity : 0.005 0.057 5603 Dihedral : 17.637 179.352 5255 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 0.01 (0.14), residues: 3833 helix: 1.25 (0.14), residues: 1308 sheet: -0.49 (0.21), residues: 578 loop : -0.65 (0.15), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 75 TYR 0.033 0.002 TYR B 797 PHE 0.027 0.002 PHE A1220 TRP 0.027 0.002 TRP B 466 HIS 0.009 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.30 (33658) covalent geometry : angle 0.72092 / 0.38 (45831) hydrogen bonds : bond 0.04608 / 3.08 ( 1412) hydrogen bonds : angle 5.46554 / 3.84 ( 3928) metal coordination : bond 0.01022 / 0.67 ( 32) metal coordination : angle 5.41051 / 3.54 ( 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 478 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 1.495 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8822 (mtm) cc_final: 0.8508 (mtt) REVERT: A 341 MET cc_start: 0.9328 (mmm) cc_final: 0.9111 (mmm) REVERT: A 444 PHE cc_start: 0.9333 (t80) cc_final: 0.8824 (t80) REVERT: A 453 MET cc_start: 0.9200 (mpp) cc_final: 0.8974 (mpp) REVERT: A 455 MET cc_start: 0.8971 (ttt) cc_final: 0.8273 (ttt) REVERT: A 456 MET cc_start: 0.9211 (ttm) cc_final: 0.8955 (ttm) REVERT: A 487 MET cc_start: 0.8895 (mtp) cc_final: 0.8042 (mtp) REVERT: A 511 ILE cc_start: 0.9298 (mp) cc_final: 0.8935 (mp) REVERT: A 521 MET cc_start: 0.9580 (ptp) cc_final: 0.9189 (mpp) REVERT: A 676 MET cc_start: 0.8918 (mmm) cc_final: 0.8602 (mmm) REVERT: A 731 ARG cc_start: 0.9438 (mmt180) cc_final: 0.9156 (mmp80) REVERT: A 748 MET cc_start: 0.9419 (mtm) cc_final: 0.8929 (mpp) REVERT: A 838 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8868 (tm-30) REVERT: A 849 MET cc_start: 0.8870 (tmm) cc_final: 0.8638 (tmm) REVERT: A 873 MET cc_start: 0.9367 (mmp) cc_final: 0.9050 (mmm) REVERT: A 874 ASP cc_start: 0.9332 (t0) cc_final: 0.8994 (t70) REVERT: A 932 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9176 (mm-30) REVERT: A 956 LEU cc_start: 0.9575 (mt) cc_final: 0.9289 (mp) REVERT: A 1019 CYS cc_start: 0.9586 (m) cc_final: 0.9274 (m) REVERT: A 1079 MET cc_start: 0.7617 (ptp) cc_final: 0.7155 (ptp) REVERT: A 1267 MET cc_start: 0.9100 (mmt) cc_final: 0.8793 (mmm) REVERT: A 1317 MET cc_start: 0.9497 (ptp) cc_final: 0.8960 (ptp) REVERT: A 1337 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8787 (pt0) REVERT: A 1368 MET cc_start: 0.9109 (ptp) cc_final: 0.8807 (ptt) REVERT: A 1404 GLU cc_start: 0.8646 (mt-10) cc_final: 0.7743 (mm-30) REVERT: B 224 GLN cc_start: 0.9641 (mt0) cc_final: 0.9407 (mp10) REVERT: B 259 TYR cc_start: 0.8772 (m-80) cc_final: 0.8147 (m-80) REVERT: B 310 MET cc_start: 0.9589 (mtp) cc_final: 0.9283 (mtp) REVERT: B 381 MET cc_start: 0.9476 (mtp) cc_final: 0.9129 (mtp) REVERT: B 521 LEU cc_start: 0.9711 (mt) cc_final: 0.9491 (mt) REVERT: B 643 ASP cc_start: 0.8487 (t0) cc_final: 0.8176 (p0) REVERT: B 698 GLU cc_start: 0.9437 (tt0) cc_final: 0.9183 (tm-30) REVERT: B 747 MET cc_start: 0.9406 (mmm) cc_final: 0.8934 (mmm) REVERT: B 762 ASN cc_start: 0.9180 (m-40) cc_final: 0.8314 (m110) REVERT: B 775 LYS cc_start: 0.9424 (mtmt) cc_final: 0.9141 (mtmm) REVERT: B 782 LEU cc_start: 0.9668 (mt) cc_final: 0.9429 (tp) REVERT: B 789 MET cc_start: 0.8414 (mmm) cc_final: 0.7817 (mmm) REVERT: B 999 MET cc_start: 0.9039 (mmt) cc_final: 0.8753 (mmt) REVERT: B 1098 MET cc_start: 0.9209 (mtm) cc_final: 0.8960 (mtm) REVERT: B 1128 LEU cc_start: 0.9286 (mt) cc_final: 0.9033 (mt) REVERT: B 1132 GLU cc_start: 0.8699 (pm20) cc_final: 0.8344 (pp20) REVERT: B 1136 ASP cc_start: 0.9260 (m-30) cc_final: 0.8598 (m-30) REVERT: B 1138 MET cc_start: 0.9466 (mmp) cc_final: 0.9222 (mmm) REVERT: B 1202 LEU cc_start: 0.9773 (tp) cc_final: 0.9512 (tp) REVERT: B 1206 GLU cc_start: 0.9655 (mt-10) cc_final: 0.9388 (mt-10) REVERT: B 1207 LEU cc_start: 0.9902 (mm) cc_final: 0.9509 (tp) REVERT: B 1208 MET cc_start: 0.9465 (mtt) cc_final: 0.9235 (mtp) REVERT: C 26 ASP cc_start: 0.9082 (p0) cc_final: 0.8743 (p0) REVERT: C 37 MET cc_start: 0.9329 (mtp) cc_final: 0.8902 (mtp) REVERT: C 166 GLU cc_start: 0.8908 (tt0) cc_final: 0.8550 (tp30) REVERT: D 119 ARG cc_start: 0.5317 (mpt180) cc_final: 0.4953 (mmp80) REVERT: E 32 GLN cc_start: 0.9261 (tt0) cc_final: 0.8774 (tp-100) REVERT: E 57 MET cc_start: 0.9338 (mtm) cc_final: 0.9099 (mtp) REVERT: E 58 MET cc_start: 0.8911 (mmm) cc_final: 0.8604 (mmm) REVERT: E 215 MET cc_start: 0.8964 (ptt) cc_final: 0.8601 (ppp) REVERT: F 103 MET cc_start: 0.9602 (mmp) cc_final: 0.9124 (mmm) REVERT: F 110 ASP cc_start: 0.9459 (m-30) cc_final: 0.9255 (t0) REVERT: F 119 ARG cc_start: 0.9560 (tpp80) cc_final: 0.9101 (tpp80) REVERT: F 122 MET cc_start: 0.9670 (mtm) cc_final: 0.9117 (mtp) REVERT: F 124 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9011 (mm-30) REVERT: G 2 PHE cc_start: 0.8934 (m-80) cc_final: 0.8731 (m-10) REVERT: G 3 PHE cc_start: 0.9138 (m-80) cc_final: 0.8552 (m-80) REVERT: G 9 LEU cc_start: 0.8299 (tp) cc_final: 0.8002 (tt) REVERT: G 47 CYS cc_start: 0.9246 (t) cc_final: 0.9024 (t) REVERT: G 60 ARG cc_start: 0.9504 (ttp80) cc_final: 0.8831 (ttp80) REVERT: G 119 LEU cc_start: 0.4827 (mp) cc_final: 0.4560 (tt) REVERT: G 171 ILE cc_start: 0.4603 (mp) cc_final: 0.4178 (mp) REVERT: H 22 LYS cc_start: 0.9493 (mttp) cc_final: 0.9039 (mmmm) REVERT: H 45 GLU cc_start: 0.8482 (mp0) cc_final: 0.7448 (mp0) REVERT: H 141 TYR cc_start: 0.9350 (m-80) cc_final: 0.8835 (m-10) REVERT: I 3 THR cc_start: 0.9421 (m) cc_final: 0.9194 (p) REVERT: I 9 ASP cc_start: 0.8674 (t70) cc_final: 0.8465 (t70) REVERT: I 26 LEU cc_start: 0.8820 (mt) cc_final: 0.8257 (pp) REVERT: I 28 GLU cc_start: 0.8553 (pm20) cc_final: 0.8349 (pm20) REVERT: I 68 LEU cc_start: 0.9397 (mt) cc_final: 0.8985 (pt) REVERT: I 110 PHE cc_start: 0.3001 (m-80) cc_final: 0.2215 (m-80) REVERT: J 49 MET cc_start: 0.9258 (tpp) cc_final: 0.8871 (mmm) REVERT: K 52 ASN cc_start: 0.9253 (m110) cc_final: 0.8909 (m110) REVERT: L 30 ILE cc_start: 0.8804 (mm) cc_final: 0.8469 (tp) REVERT: L 56 LEU cc_start: 0.8663 (mt) cc_final: 0.8364 (mt) REVERT: L 57 LEU cc_start: 0.8811 (mp) cc_final: 0.8609 (mp) REVERT: L 66 GLN cc_start: 0.9290 (pp30) cc_final: 0.9051 (pp30) REVERT: L 67 PHE cc_start: 0.9050 (m-80) cc_final: 0.8810 (m-80) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.2182 time to fit residues: 170.8748 Evaluate side-chains 385 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 14 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.041719 restraints weight = 170349.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.042966 restraints weight = 97557.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043821 restraints weight = 67153.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.044362 restraints weight = 51861.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.044789 restraints weight = 43800.696| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33690 Z= 0.155 Angle : 0.632 10.779 45876 Z= 0.325 Chirality : 0.045 0.372 5155 Planarity : 0.004 0.052 5603 Dihedral : 17.616 179.641 5255 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.67 % Rotamer: Outliers : 0.03 % Allowed : 2.19 % 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: 0.20 (0.14), residues: 3833 helix: 1.49 (0.14), residues: 1312 sheet: -0.53 (0.21), residues: 587 loop : -0.56 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 75 TYR 0.021 0.001 TYR D 147 PHE 0.025 0.002 PHE A 444 TRP 0.026 0.001 TRP B 466 HIS 0.006 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (33658) covalent geometry : angle 0.61529 / 0.32 (45831) hydrogen bonds : bond 0.03807 / 2.53 ( 1412) hydrogen bonds : angle 5.14855 / 3.60 ( 3928) metal coordination : bond 0.00837 / 0.58 ( 32) metal coordination : angle 4.63768 / 3.00 ( 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 515 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 1.442 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8737 (mtm) cc_final: 0.8419 (mtt) REVERT: A 341 MET cc_start: 0.9313 (mmm) cc_final: 0.9035 (mmm) REVERT: A 455 MET cc_start: 0.8954 (ttt) cc_final: 0.8067 (ttt) REVERT: A 456 MET cc_start: 0.9326 (ttm) cc_final: 0.9110 (ttm) REVERT: A 487 MET cc_start: 0.8510 (mtp) cc_final: 0.8099 (mtt) REVERT: A 510 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8603 (mp10) REVERT: A 511 ILE cc_start: 0.9180 (mp) cc_final: 0.8865 (mp) REVERT: A 521 MET cc_start: 0.9585 (ptp) cc_final: 0.9225 (mpp) REVERT: A 676 MET cc_start: 0.8909 (mmm) cc_final: 0.8574 (mmm) REVERT: A 734 GLU cc_start: 0.9310 (tt0) cc_final: 0.9082 (mt-10) REVERT: A 748 MET cc_start: 0.9440 (mtm) cc_final: 0.8936 (mtp) REVERT: A 761 MET cc_start: 0.9420 (mtp) cc_final: 0.9190 (mpp) REVERT: A 838 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8919 (tm-30) REVERT: A 846 GLU cc_start: 0.9122 (pt0) cc_final: 0.8861 (pt0) REVERT: A 873 MET cc_start: 0.9306 (mmp) cc_final: 0.9071 (mmm) REVERT: A 874 ASP cc_start: 0.9321 (t0) cc_final: 0.8959 (t70) REVERT: A 932 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9128 (mm-30) REVERT: A 956 LEU cc_start: 0.9585 (mt) cc_final: 0.9283 (mp) REVERT: A 1079 MET cc_start: 0.7377 (ptp) cc_final: 0.6940 (ptp) REVERT: A 1144 LYS cc_start: 0.9221 (ttmm) cc_final: 0.9005 (ttpt) REVERT: A 1267 MET cc_start: 0.9050 (mmt) cc_final: 0.8800 (mmp) REVERT: A 1317 MET cc_start: 0.9500 (ptp) cc_final: 0.8919 (ptp) REVERT: A 1337 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8782 (pt0) REVERT: A 1373 ASP cc_start: 0.9304 (m-30) cc_final: 0.8865 (m-30) REVERT: A 1404 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7756 (mm-30) REVERT: A 1417 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 1433 MET cc_start: 0.7864 (tpp) cc_final: 0.7539 (tpp) REVERT: B 224 GLN cc_start: 0.9616 (mt0) cc_final: 0.9403 (mp10) REVERT: B 259 TYR cc_start: 0.8715 (m-80) cc_final: 0.8084 (m-80) REVERT: B 310 MET cc_start: 0.9522 (mtp) cc_final: 0.9237 (mtp) REVERT: B 381 MET cc_start: 0.9467 (mtp) cc_final: 0.9103 (mtp) REVERT: B 521 LEU cc_start: 0.9728 (mt) cc_final: 0.9467 (mt) REVERT: B 526 GLU cc_start: 0.7759 (tp30) cc_final: 0.7453 (tp30) REVERT: B 625 LYS cc_start: 0.9531 (mppt) cc_final: 0.9239 (mmtp) REVERT: B 698 GLU cc_start: 0.9401 (tt0) cc_final: 0.9156 (tm-30) REVERT: B 747 MET cc_start: 0.9365 (mmm) cc_final: 0.8945 (mmm) REVERT: B 762 ASN cc_start: 0.9101 (m-40) cc_final: 0.8311 (m-40) REVERT: B 775 LYS cc_start: 0.9392 (mtmt) cc_final: 0.9134 (mtmm) REVERT: B 789 MET cc_start: 0.8287 (mmm) cc_final: 0.7884 (mmm) REVERT: B 1072 MET cc_start: 0.8888 (tpt) cc_final: 0.8411 (tpp) REVERT: B 1132 GLU cc_start: 0.8643 (pm20) cc_final: 0.8323 (pp20) REVERT: B 1136 ASP cc_start: 0.9255 (m-30) cc_final: 0.8615 (m-30) REVERT: B 1138 MET cc_start: 0.9372 (mmp) cc_final: 0.9156 (mmm) REVERT: B 1152 MET cc_start: 0.8992 (mmt) cc_final: 0.8687 (mmt) REVERT: B 1202 LEU cc_start: 0.9744 (tp) cc_final: 0.9505 (tp) REVERT: B 1206 GLU cc_start: 0.9628 (mt-10) cc_final: 0.9368 (mt-10) REVERT: C 26 ASP cc_start: 0.9051 (p0) cc_final: 0.8716 (p0) REVERT: C 29 MET cc_start: 0.9453 (ttm) cc_final: 0.9063 (mtm) REVERT: C 37 MET cc_start: 0.9305 (mtp) cc_final: 0.8872 (mmm) REVERT: C 166 GLU cc_start: 0.8824 (tt0) cc_final: 0.8472 (tp30) REVERT: D 119 ARG cc_start: 0.5322 (mpt180) cc_final: 0.4935 (mmp80) REVERT: E 32 GLN cc_start: 0.9243 (tt0) cc_final: 0.8743 (tp-100) REVERT: E 50 MET cc_start: 0.9451 (ptp) cc_final: 0.9109 (ppp) REVERT: E 57 MET cc_start: 0.9335 (mtm) cc_final: 0.9069 (mtp) REVERT: E 215 MET cc_start: 0.8955 (ptt) cc_final: 0.8581 (ppp) REVERT: F 85 MET cc_start: 0.9592 (tmm) cc_final: 0.9121 (tmm) REVERT: F 87 LYS cc_start: 0.9593 (pttm) cc_final: 0.9245 (pttm) REVERT: F 103 MET cc_start: 0.9586 (mmp) cc_final: 0.9206 (mmm) REVERT: F 110 ASP cc_start: 0.9440 (m-30) cc_final: 0.8956 (t0) REVERT: F 118 LEU cc_start: 0.9722 (tp) cc_final: 0.9506 (tp) REVERT: F 119 ARG cc_start: 0.9601 (tpp80) cc_final: 0.9190 (tpp80) REVERT: F 122 MET cc_start: 0.9685 (mtm) cc_final: 0.9119 (mtp) REVERT: F 124 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9021 (mm-30) REVERT: G 3 PHE cc_start: 0.9109 (m-80) cc_final: 0.8490 (m-10) REVERT: G 9 LEU cc_start: 0.8333 (tp) cc_final: 0.7992 (tt) REVERT: G 47 CYS cc_start: 0.9287 (t) cc_final: 0.9084 (t) REVERT: G 60 ARG cc_start: 0.9465 (ttp80) cc_final: 0.8825 (ttp80) REVERT: G 119 LEU cc_start: 0.4870 (mp) cc_final: 0.4397 (tp) REVERT: H 22 LYS cc_start: 0.9455 (mttp) cc_final: 0.9089 (mmmm) REVERT: H 45 GLU cc_start: 0.8520 (mp0) cc_final: 0.7717 (mp0) REVERT: H 105 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 116 TYR cc_start: 0.8954 (m-80) cc_final: 0.8680 (m-80) REVERT: H 123 MET cc_start: 0.8700 (tmm) cc_final: 0.8397 (tmm) REVERT: H 141 TYR cc_start: 0.9262 (m-80) cc_final: 0.9010 (m-80) REVERT: I 3 THR cc_start: 0.9398 (m) cc_final: 0.9137 (p) REVERT: I 9 ASP cc_start: 0.8713 (t70) cc_final: 0.8513 (t70) REVERT: I 26 LEU cc_start: 0.8825 (mt) cc_final: 0.8264 (pp) REVERT: I 28 GLU cc_start: 0.8484 (pm20) cc_final: 0.8262 (pm20) REVERT: I 68 LEU cc_start: 0.9384 (mt) cc_final: 0.8933 (pt) REVERT: I 110 PHE cc_start: 0.3164 (m-80) cc_final: 0.2475 (m-80) REVERT: J 21 TYR cc_start: 0.9510 (t80) cc_final: 0.9093 (t80) REVERT: J 27 GLU cc_start: 0.8446 (pp20) cc_final: 0.8197 (pp20) REVERT: J 49 MET cc_start: 0.9260 (tpp) cc_final: 0.8825 (mmm) REVERT: K 22 ASP cc_start: 0.9364 (t0) cc_final: 0.8893 (p0) REVERT: K 52 ASN cc_start: 0.9203 (m110) cc_final: 0.8890 (m110) REVERT: K 64 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7412 (mt-10) REVERT: L 30 ILE cc_start: 0.8870 (mm) cc_final: 0.8486 (tp) REVERT: L 56 LEU cc_start: 0.8733 (mt) cc_final: 0.8374 (mt) REVERT: L 57 LEU cc_start: 0.8786 (mp) cc_final: 0.8582 (mp) REVERT: L 63 ARG cc_start: 0.8811 (mtm110) cc_final: 0.8389 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 515 average time/residue: 0.2187 time to fit residues: 184.4856 Evaluate side-chains 403 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 273 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS K 92 ASN ** L 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 = 0.3118 r_free = 0.3118 target = 0.059455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.041120 restraints weight = 171839.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.042347 restraints weight = 98555.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.043178 restraints weight = 67759.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.043794 restraints weight = 52546.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.044099 restraints weight = 43915.382| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 33690 Z= 0.202 Angle : 0.655 13.748 45876 Z= 0.335 Chirality : 0.044 0.371 5155 Planarity : 0.004 0.077 5603 Dihedral : 17.622 179.622 5255 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.96 % 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: 1.48 (0.14), residues: 1315 sheet: -0.54 (0.21), residues: 594 loop : -0.57 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 52 TYR 0.025 0.001 TYR D 147 PHE 0.031 0.002 PHE B 37 TRP 0.026 0.001 TRP B 466 HIS 0.007 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (33658) covalent geometry : angle 0.63567 / 0.33 (45831) hydrogen bonds : bond 0.03843 / 2.56 ( 1412) hydrogen bonds : angle 5.12194 / 3.57 ( 3928) metal coordination : bond 0.00883 / 0.58 ( 32) metal coordination : angle 5.04660 / 3.19 ( 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 480 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 1.317 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8741 (mtm) cc_final: 0.8421 (mtt) REVERT: A 234 MET cc_start: 0.9355 (tpp) cc_final: 0.8966 (tpp) REVERT: A 341 MET cc_start: 0.9330 (mmm) cc_final: 0.9077 (mmm) REVERT: A 437 MET cc_start: 0.9050 (ptp) cc_final: 0.8632 (mpp) REVERT: A 453 MET cc_start: 0.9215 (mpp) cc_final: 0.8884 (mpp) REVERT: A 455 MET cc_start: 0.8930 (ttt) cc_final: 0.8062 (ttt) REVERT: A 456 MET cc_start: 0.9208 (ttm) cc_final: 0.8700 (ttm) REVERT: A 487 MET cc_start: 0.8736 (mtp) cc_final: 0.8429 (mtt) REVERT: A 521 MET cc_start: 0.9599 (ptp) cc_final: 0.9295 (ptp) REVERT: A 676 MET cc_start: 0.8984 (mmm) cc_final: 0.8645 (mmm) REVERT: A 731 ARG cc_start: 0.9384 (mmt180) cc_final: 0.9102 (mmp80) REVERT: A 748 MET cc_start: 0.9443 (mtm) cc_final: 0.8966 (mtp) REVERT: A 838 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8961 (tm-30) REVERT: A 846 GLU cc_start: 0.9136 (pt0) cc_final: 0.8867 (pt0) REVERT: A 849 MET cc_start: 0.8824 (tmm) cc_final: 0.8581 (tmm) REVERT: A 873 MET cc_start: 0.9324 (mmp) cc_final: 0.9089 (mmm) REVERT: A 874 ASP cc_start: 0.9353 (t0) cc_final: 0.8987 (t70) REVERT: A 932 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9151 (mm-30) REVERT: A 956 LEU cc_start: 0.9587 (mt) cc_final: 0.9321 (mp) REVERT: A 1019 CYS cc_start: 0.9598 (m) cc_final: 0.9291 (m) REVERT: A 1079 MET cc_start: 0.7459 (ptp) cc_final: 0.6977 (ptp) REVERT: A 1308 THR cc_start: 0.9285 (p) cc_final: 0.9073 (t) REVERT: A 1317 MET cc_start: 0.9483 (ptp) cc_final: 0.9261 (ptm) REVERT: A 1337 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8816 (pt0) REVERT: A 1368 MET cc_start: 0.9087 (ptp) cc_final: 0.8626 (ptt) REVERT: A 1373 ASP cc_start: 0.9333 (m-30) cc_final: 0.8898 (m-30) REVERT: A 1404 GLU cc_start: 0.8771 (mt-10) cc_final: 0.7974 (mm-30) REVERT: A 1417 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8457 (mt-10) REVERT: A 1433 MET cc_start: 0.7966 (tpp) cc_final: 0.7610 (tpp) REVERT: B 224 GLN cc_start: 0.9638 (mt0) cc_final: 0.9408 (mp10) REVERT: B 259 TYR cc_start: 0.8806 (m-80) cc_final: 0.8166 (m-80) REVERT: B 381 MET cc_start: 0.9472 (mtp) cc_final: 0.9119 (mtp) REVERT: B 521 LEU cc_start: 0.9722 (mt) cc_final: 0.9461 (mt) REVERT: B 526 GLU cc_start: 0.7783 (tp30) cc_final: 0.7065 (tp30) REVERT: B 625 LYS cc_start: 0.9570 (mppt) cc_final: 0.9256 (mmtp) REVERT: B 643 ASP cc_start: 0.8805 (t0) cc_final: 0.8435 (p0) REVERT: B 698 GLU cc_start: 0.9419 (tt0) cc_final: 0.9130 (tm-30) REVERT: B 747 MET cc_start: 0.9388 (mmm) cc_final: 0.8961 (mmm) REVERT: B 762 ASN cc_start: 0.9125 (m-40) cc_final: 0.8265 (m110) REVERT: B 775 LYS cc_start: 0.9425 (mtmt) cc_final: 0.9080 (mtmt) REVERT: B 789 MET cc_start: 0.8309 (mmm) cc_final: 0.7982 (mmm) REVERT: B 821 GLN cc_start: 0.9201 (mp10) cc_final: 0.8624 (mp10) REVERT: B 1028 GLU cc_start: 0.9523 (tt0) cc_final: 0.8868 (tm-30) REVERT: B 1128 LEU cc_start: 0.9220 (mt) cc_final: 0.8978 (mt) REVERT: B 1132 GLU cc_start: 0.8696 (pm20) cc_final: 0.8374 (pp20) REVERT: B 1136 ASP cc_start: 0.9230 (m-30) cc_final: 0.8562 (m-30) REVERT: B 1138 MET cc_start: 0.9431 (mmp) cc_final: 0.9200 (mmm) REVERT: B 1202 LEU cc_start: 0.9754 (tp) cc_final: 0.9511 (tp) REVERT: B 1206 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9353 (mt-10) REVERT: B 1208 MET cc_start: 0.9443 (mtt) cc_final: 0.9237 (mtp) REVERT: C 26 ASP cc_start: 0.9053 (p0) cc_final: 0.8725 (p0) REVERT: C 29 MET cc_start: 0.9477 (ttm) cc_final: 0.9081 (mtm) REVERT: C 37 MET cc_start: 0.9358 (mtp) cc_final: 0.9069 (mtp) REVERT: C 166 GLU cc_start: 0.8874 (tt0) cc_final: 0.8483 (tp30) REVERT: D 119 ARG cc_start: 0.5563 (mpt180) cc_final: 0.5190 (mmp80) REVERT: E 32 GLN cc_start: 0.9281 (tt0) cc_final: 0.8772 (tp-100) REVERT: E 57 MET cc_start: 0.9362 (mtm) cc_final: 0.9162 (mtp) REVERT: E 215 MET cc_start: 0.8964 (ptt) cc_final: 0.8579 (ppp) REVERT: F 85 MET cc_start: 0.9616 (tmm) cc_final: 0.9166 (tmm) REVERT: F 103 MET cc_start: 0.9574 (mmp) cc_final: 0.9187 (mmm) REVERT: F 118 LEU cc_start: 0.9736 (tp) cc_final: 0.9531 (tp) REVERT: F 119 ARG cc_start: 0.9610 (tpp80) cc_final: 0.9199 (tpp80) REVERT: F 122 MET cc_start: 0.9681 (mtm) cc_final: 0.9137 (mtp) REVERT: G 3 PHE cc_start: 0.9122 (m-80) cc_final: 0.8542 (m-80) REVERT: G 9 LEU cc_start: 0.8326 (tp) cc_final: 0.8001 (tt) REVERT: G 46 LEU cc_start: 0.9733 (mm) cc_final: 0.9509 (mm) REVERT: G 47 CYS cc_start: 0.9269 (t) cc_final: 0.8925 (t) REVERT: G 60 ARG cc_start: 0.9449 (ttp80) cc_final: 0.8985 (ttp80) REVERT: G 82 PHE cc_start: 0.6502 (m-10) cc_final: 0.6272 (m-80) REVERT: H 22 LYS cc_start: 0.9460 (mttp) cc_final: 0.9101 (mmmm) REVERT: H 45 GLU cc_start: 0.8632 (mp0) cc_final: 0.7769 (mp0) REVERT: H 105 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8006 (tm-30) REVERT: H 116 TYR cc_start: 0.8983 (m-80) cc_final: 0.8690 (m-80) REVERT: H 123 MET cc_start: 0.8792 (tmm) cc_final: 0.8458 (tmm) REVERT: H 141 TYR cc_start: 0.9277 (m-80) cc_final: 0.9045 (m-80) REVERT: I 3 THR cc_start: 0.9387 (m) cc_final: 0.9101 (p) REVERT: I 68 LEU cc_start: 0.9390 (mt) cc_final: 0.8936 (pt) REVERT: I 110 PHE cc_start: 0.2864 (m-80) cc_final: 0.2135 (m-80) REVERT: J 21 TYR cc_start: 0.9562 (t80) cc_final: 0.9110 (t80) REVERT: J 49 MET cc_start: 0.9256 (tpp) cc_final: 0.8800 (mmm) REVERT: K 7 PHE cc_start: 0.9133 (p90) cc_final: 0.8924 (p90) REVERT: K 17 SER cc_start: 0.9357 (m) cc_final: 0.9136 (p) REVERT: K 49 GLU cc_start: 0.9018 (tp30) cc_final: 0.8783 (tp30) REVERT: K 106 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9346 (mt-10) REVERT: L 30 ILE cc_start: 0.8881 (mm) cc_final: 0.8603 (mm) REVERT: L 55 ILE cc_start: 0.9579 (mp) cc_final: 0.9338 (mp) REVERT: L 56 LEU cc_start: 0.8598 (mt) cc_final: 0.8134 (mt) REVERT: L 67 PHE cc_start: 0.8932 (m-80) cc_final: 0.8585 (m-80) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.2159 time to fit residues: 170.5202 Evaluate side-chains 407 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 353 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.041341 restraints weight = 172156.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.042592 restraints weight = 98217.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.043439 restraints weight = 67653.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.043979 restraints weight = 52364.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.044396 restraints weight = 44255.416| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33690 Z= 0.171 Angle : 0.637 10.859 45876 Z= 0.326 Chirality : 0.044 0.372 5155 Planarity : 0.004 0.053 5603 Dihedral : 17.620 179.471 5255 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % 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: 0.22 (0.14), residues: 3833 helix: 1.50 (0.14), residues: 1316 sheet: -0.59 (0.21), residues: 592 loop : -0.52 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 75 TYR 0.024 0.001 TYR D 147 PHE 0.032 0.002 PHE G 82 TRP 0.028 0.001 TRP B 466 HIS 0.007 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (33658) covalent geometry : angle 0.62021 / 0.33 (45831) hydrogen bonds : bond 0.03678 / 2.44 ( 1412) hydrogen bonds : angle 4.99950 / 3.49 ( 3928) metal coordination : bond 0.00852 / 0.58 ( 32) metal coordination : angle 4.63140 / 2.97 ( 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 476 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 1.234 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: 0.8723 (mtm) cc_final: 0.8405 (mtt) REVERT: A 341 MET cc_start: 0.9328 (mmm) cc_final: 0.9049 (mmm) REVERT: A 444 PHE cc_start: 0.9329 (t80) cc_final: 0.8696 (t80) REVERT: A 453 MET cc_start: 0.9228 (mpp) cc_final: 0.8898 (mpp) REVERT: A 455 MET cc_start: 0.8995 (ttt) cc_final: 0.8133 (ttt) REVERT: A 456 MET cc_start: 0.9205 (ttm) cc_final: 0.8604 (ttm) REVERT: A 487 MET cc_start: 0.8856 (mtp) cc_final: 0.8131 (mtp) REVERT: A 511 ILE cc_start: 0.9181 (mp) cc_final: 0.8965 (mp) REVERT: A 521 MET cc_start: 0.9592 (ptp) cc_final: 0.9266 (ptp) REVERT: A 676 MET cc_start: 0.8995 (mmm) cc_final: 0.8648 (mmm) REVERT: A 731 ARG cc_start: 0.9388 (mmt180) cc_final: 0.9084 (mmp80) REVERT: A 734 GLU cc_start: 0.9315 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 748 MET cc_start: 0.9438 (mtm) cc_final: 0.8999 (mpp) REVERT: A 838 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8953 (tm-30) REVERT: A 846 GLU cc_start: 0.9144 (pt0) cc_final: 0.8842 (pt0) REVERT: A 849 MET cc_start: 0.8851 (tmm) cc_final: 0.8643 (tmm) REVERT: A 873 MET cc_start: 0.9302 (mmp) cc_final: 0.9071 (mmm) REVERT: A 874 ASP cc_start: 0.9290 (t0) cc_final: 0.8953 (t70) REVERT: A 932 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9179 (mm-30) REVERT: A 956 LEU cc_start: 0.9590 (mt) cc_final: 0.9286 (mp) REVERT: A 1079 MET cc_start: 0.7243 (ptp) cc_final: 0.6758 (ptp) REVERT: A 1317 MET cc_start: 0.9460 (ptp) cc_final: 0.9219 (ptm) REVERT: A 1337 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8852 (pt0) REVERT: A 1373 ASP cc_start: 0.9313 (m-30) cc_final: 0.8858 (m-30) REVERT: A 1404 GLU cc_start: 0.8768 (mt-10) cc_final: 0.7983 (mm-30) REVERT: A 1417 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 173 MET cc_start: 0.9346 (tpp) cc_final: 0.9142 (tpp) REVERT: B 224 GLN cc_start: 0.9638 (mt0) cc_final: 0.9408 (mp10) REVERT: B 259 TYR cc_start: 0.8796 (m-80) cc_final: 0.8174 (m-80) REVERT: B 381 MET cc_start: 0.9472 (mtp) cc_final: 0.9121 (mtp) REVERT: B 427 ASP cc_start: 0.9277 (m-30) cc_final: 0.9065 (m-30) REVERT: B 521 LEU cc_start: 0.9718 (mt) cc_final: 0.9456 (mt) REVERT: B 621 GLU cc_start: 0.9222 (mp0) cc_final: 0.9010 (mp0) REVERT: B 643 ASP cc_start: 0.8783 (t0) cc_final: 0.8424 (p0) REVERT: B 698 GLU cc_start: 0.9403 (tt0) cc_final: 0.9139 (tm-30) REVERT: B 747 MET cc_start: 0.9375 (mmm) cc_final: 0.8955 (mmm) REVERT: B 762 ASN cc_start: 0.9093 (m-40) cc_final: 0.8243 (m-40) REVERT: B 775 LYS cc_start: 0.9395 (mtmt) cc_final: 0.9128 (mtmm) REVERT: B 821 GLN cc_start: 0.9152 (mp10) cc_final: 0.8572 (mp10) REVERT: B 999 MET cc_start: 0.8967 (mmt) cc_final: 0.8754 (mmt) REVERT: B 1028 GLU cc_start: 0.9546 (tt0) cc_final: 0.8861 (tm-30) REVERT: B 1128 LEU cc_start: 0.9220 (mt) cc_final: 0.8964 (mt) REVERT: B 1132 GLU cc_start: 0.8726 (pm20) cc_final: 0.8370 (pp20) REVERT: B 1136 ASP cc_start: 0.9231 (m-30) cc_final: 0.8546 (m-30) REVERT: B 1202 LEU cc_start: 0.9746 (tp) cc_final: 0.9487 (tp) REVERT: B 1206 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9362 (mt-10) REVERT: B 1208 MET cc_start: 0.9436 (mtt) cc_final: 0.9214 (mtp) REVERT: C 26 ASP cc_start: 0.9046 (p0) cc_final: 0.8736 (p0) REVERT: C 29 MET cc_start: 0.9478 (ttm) cc_final: 0.9098 (mtm) REVERT: C 37 MET cc_start: 0.9372 (mtp) cc_final: 0.9113 (mtp) REVERT: C 166 GLU cc_start: 0.8885 (tt0) cc_final: 0.8429 (tp30) REVERT: D 119 ARG cc_start: 0.5558 (mpt180) cc_final: 0.5181 (mmp80) REVERT: E 32 GLN cc_start: 0.9280 (tt0) cc_final: 0.8770 (tp-100) REVERT: E 57 MET cc_start: 0.9377 (mtm) cc_final: 0.9170 (mtp) REVERT: E 58 MET cc_start: 0.9281 (mmm) cc_final: 0.8868 (mmm) REVERT: E 215 MET cc_start: 0.8965 (ptt) cc_final: 0.8568 (ppp) REVERT: F 85 MET cc_start: 0.9627 (tmm) cc_final: 0.9203 (tmm) REVERT: F 99 LEU cc_start: 0.9666 (tp) cc_final: 0.9447 (tp) REVERT: F 103 MET cc_start: 0.9588 (mmp) cc_final: 0.9168 (mmm) REVERT: F 118 LEU cc_start: 0.9721 (tp) cc_final: 0.9502 (tp) REVERT: F 119 ARG cc_start: 0.9669 (tpp80) cc_final: 0.9135 (tpp80) REVERT: F 122 MET cc_start: 0.9684 (mtm) cc_final: 0.9127 (mtp) REVERT: G 3 PHE cc_start: 0.9218 (m-80) cc_final: 0.8492 (m-80) REVERT: G 9 LEU cc_start: 0.8311 (tp) cc_final: 0.7928 (tt) REVERT: G 47 CYS cc_start: 0.9282 (t) cc_final: 0.8963 (t) REVERT: G 60 ARG cc_start: 0.9430 (ttp80) cc_final: 0.8757 (ttp80) REVERT: G 99 PHE cc_start: 0.6767 (p90) cc_final: 0.6548 (p90) REVERT: H 22 LYS cc_start: 0.9462 (mttp) cc_final: 0.9114 (mmmm) REVERT: H 45 GLU cc_start: 0.8554 (mp0) cc_final: 0.7702 (mp0) REVERT: H 105 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 116 TYR cc_start: 0.9009 (m-80) cc_final: 0.8672 (m-80) REVERT: H 123 MET cc_start: 0.8821 (tmm) cc_final: 0.8468 (tmm) REVERT: I 3 THR cc_start: 0.9395 (m) cc_final: 0.9112 (p) REVERT: I 9 ASP cc_start: 0.8793 (t70) cc_final: 0.8577 (t70) REVERT: I 68 LEU cc_start: 0.9385 (mt) cc_final: 0.8916 (pt) REVERT: I 110 PHE cc_start: 0.3189 (m-80) cc_final: 0.2293 (m-80) REVERT: J 21 TYR cc_start: 0.9564 (t80) cc_final: 0.9085 (t80) REVERT: J 49 MET cc_start: 0.9235 (tpp) cc_final: 0.8774 (mmm) REVERT: K 7 PHE cc_start: 0.9114 (p90) cc_final: 0.8875 (p90) REVERT: K 22 ASP cc_start: 0.9385 (t0) cc_final: 0.8905 (p0) REVERT: K 49 GLU cc_start: 0.9063 (tp30) cc_final: 0.8845 (tp30) REVERT: K 75 ILE cc_start: 0.9577 (mp) cc_final: 0.9375 (mp) REVERT: L 30 ILE cc_start: 0.8906 (mm) cc_final: 0.8505 (tp) REVERT: L 56 LEU cc_start: 0.8681 (mt) cc_final: 0.8156 (mt) REVERT: L 57 LEU cc_start: 0.8785 (mp) cc_final: 0.8524 (mp) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.2178 time to fit residues: 171.1318 Evaluate side-chains 401 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 87 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 272 optimal weight: 0.0050 chunk 377 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 516 ASN B 794 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.041838 restraints weight = 170284.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.043088 restraints weight = 97154.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043949 restraints weight = 66725.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.044538 restraints weight = 51533.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.044876 restraints weight = 43329.295| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33690 Z= 0.131 Angle : 0.632 12.918 45876 Z= 0.322 Chirality : 0.044 0.374 5155 Planarity : 0.004 0.059 5603 Dihedral : 17.576 179.613 5255 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3833 helix: 1.59 (0.15), residues: 1307 sheet: -0.46 (0.20), residues: 608 loop : -0.42 (0.15), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 52 TYR 0.026 0.001 TYR B 797 PHE 0.024 0.002 PHE A 444 TRP 0.028 0.001 TRP B 466 HIS 0.011 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (33658) covalent geometry : angle 0.61471 / 0.32 (45831) hydrogen bonds : bond 0.03472 / 2.29 ( 1412) hydrogen bonds : angle 4.84676 / 3.38 ( 3928) metal coordination : bond 0.00898 / 0.61 ( 32) metal coordination : angle 4.71233 / 3.28 ( 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 495 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 494 time to evaluate : 1.259 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8700 (mtm) cc_final: 0.8399 (mtt) REVERT: A 234 MET cc_start: 0.9230 (tpp) cc_final: 0.8951 (tpp) REVERT: A 341 MET cc_start: 0.9316 (mmm) cc_final: 0.9041 (mmm) REVERT: A 437 MET cc_start: 0.9189 (ptp) cc_final: 0.8766 (mpp) REVERT: A 444 PHE cc_start: 0.9110 (t80) cc_final: 0.8812 (t80) REVERT: A 453 MET cc_start: 0.9197 (mpp) cc_final: 0.8859 (mpp) REVERT: A 455 MET cc_start: 0.8861 (ttt) cc_final: 0.8258 (ttt) REVERT: A 456 MET cc_start: 0.9222 (ttm) cc_final: 0.8570 (ttm) REVERT: A 487 MET cc_start: 0.8553 (mtp) cc_final: 0.7936 (mtp) REVERT: A 511 ILE cc_start: 0.9199 (mp) cc_final: 0.8978 (mp) REVERT: A 521 MET cc_start: 0.9585 (ptp) cc_final: 0.9268 (ptp) REVERT: A 676 MET cc_start: 0.8996 (mmm) cc_final: 0.8642 (mmm) REVERT: A 731 ARG cc_start: 0.9380 (mmt180) cc_final: 0.9109 (mmp80) REVERT: A 734 GLU cc_start: 0.9321 (tt0) cc_final: 0.8640 (tm-30) REVERT: A 748 MET cc_start: 0.9455 (mtm) cc_final: 0.8911 (mtp) REVERT: A 838 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8940 (tm-30) REVERT: A 846 GLU cc_start: 0.9098 (pt0) cc_final: 0.8793 (pt0) REVERT: A 873 MET cc_start: 0.9248 (mmp) cc_final: 0.9031 (mmm) REVERT: A 874 ASP cc_start: 0.9265 (t0) cc_final: 0.8765 (t70) REVERT: A 932 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9152 (mm-30) REVERT: A 956 LEU cc_start: 0.9575 (mt) cc_final: 0.9281 (mp) REVERT: A 1062 GLU cc_start: 0.9324 (tt0) cc_final: 0.9022 (mm-30) REVERT: A 1144 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8971 (ttpt) REVERT: A 1267 MET cc_start: 0.9140 (mmp) cc_final: 0.8893 (mmp) REVERT: A 1308 THR cc_start: 0.9297 (p) cc_final: 0.9076 (t) REVERT: A 1317 MET cc_start: 0.9431 (ptp) cc_final: 0.9182 (ptm) REVERT: A 1337 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8817 (pt0) REVERT: A 1373 ASP cc_start: 0.9290 (m-30) cc_final: 0.8829 (m-30) REVERT: A 1375 MET cc_start: 0.9419 (mmt) cc_final: 0.8909 (mmm) REVERT: A 1393 ASN cc_start: 0.8988 (p0) cc_final: 0.8542 (t0) REVERT: A 1404 GLU cc_start: 0.8742 (mt-10) cc_final: 0.7946 (mm-30) REVERT: A 1417 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 173 MET cc_start: 0.9321 (tpp) cc_final: 0.9020 (tpt) REVERT: B 224 GLN cc_start: 0.9633 (mt0) cc_final: 0.9406 (mp10) REVERT: B 381 MET cc_start: 0.9473 (mtp) cc_final: 0.9120 (mtp) REVERT: B 521 LEU cc_start: 0.9718 (mt) cc_final: 0.9454 (mt) REVERT: B 643 ASP cc_start: 0.8709 (t0) cc_final: 0.8377 (p0) REVERT: B 698 GLU cc_start: 0.9344 (tt0) cc_final: 0.9113 (tm-30) REVERT: B 747 MET cc_start: 0.9354 (mmm) cc_final: 0.8940 (mmm) REVERT: B 762 ASN cc_start: 0.9000 (m-40) cc_final: 0.8107 (m-40) REVERT: B 775 LYS cc_start: 0.9367 (mtmt) cc_final: 0.9092 (mtmm) REVERT: B 821 GLN cc_start: 0.9127 (mp10) cc_final: 0.8139 (mp10) REVERT: B 999 MET cc_start: 0.8953 (mmt) cc_final: 0.8692 (mmt) REVERT: B 1128 LEU cc_start: 0.9235 (mt) cc_final: 0.9000 (mt) REVERT: B 1132 GLU cc_start: 0.8673 (pm20) cc_final: 0.8302 (pp20) REVERT: B 1136 ASP cc_start: 0.9201 (m-30) cc_final: 0.8474 (m-30) REVERT: B 1152 MET cc_start: 0.8990 (mmt) cc_final: 0.8767 (mmt) REVERT: B 1202 LEU cc_start: 0.9735 (tp) cc_final: 0.9506 (tp) REVERT: C 26 ASP cc_start: 0.9039 (p0) cc_final: 0.8718 (p0) REVERT: C 29 MET cc_start: 0.9471 (ttm) cc_final: 0.9099 (mtm) REVERT: C 37 MET cc_start: 0.9342 (mtp) cc_final: 0.9056 (mtp) REVERT: C 166 GLU cc_start: 0.8842 (tt0) cc_final: 0.8374 (tp30) REVERT: D 119 ARG cc_start: 0.5544 (mpt180) cc_final: 0.5169 (mmp80) REVERT: E 32 GLN cc_start: 0.9268 (tt0) cc_final: 0.8756 (tp-100) REVERT: E 57 MET cc_start: 0.9409 (mtm) cc_final: 0.9182 (mtp) REVERT: E 58 MET cc_start: 0.9236 (mmm) cc_final: 0.8762 (mmm) REVERT: E 215 MET cc_start: 0.8948 (ptt) cc_final: 0.8560 (ppp) REVERT: F 85 MET cc_start: 0.9627 (tmm) cc_final: 0.9200 (tmm) REVERT: F 88 TYR cc_start: 0.9291 (m-10) cc_final: 0.8757 (m-10) REVERT: F 99 LEU cc_start: 0.9671 (tp) cc_final: 0.9435 (tp) REVERT: F 103 MET cc_start: 0.9572 (mmp) cc_final: 0.9139 (mmm) REVERT: F 118 LEU cc_start: 0.9716 (tp) cc_final: 0.9485 (tp) REVERT: F 119 ARG cc_start: 0.9611 (tpp80) cc_final: 0.9176 (tpp80) REVERT: F 122 MET cc_start: 0.9665 (mtm) cc_final: 0.9102 (mtp) REVERT: F 123 LYS cc_start: 0.9430 (ttpp) cc_final: 0.9148 (tmmt) REVERT: F 124 GLU cc_start: 0.9278 (tp30) cc_final: 0.8962 (mm-30) REVERT: G 3 PHE cc_start: 0.9222 (m-80) cc_final: 0.8524 (m-80) REVERT: G 22 MET cc_start: 0.8617 (ptt) cc_final: 0.8119 (ptp) REVERT: G 47 CYS cc_start: 0.9320 (t) cc_final: 0.9055 (t) REVERT: G 60 ARG cc_start: 0.9413 (ttp80) cc_final: 0.8933 (ttp80) REVERT: H 22 LYS cc_start: 0.9463 (mttp) cc_final: 0.9101 (mmmm) REVERT: H 45 GLU cc_start: 0.8545 (mp0) cc_final: 0.7815 (mp0) REVERT: H 105 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8068 (tm-30) REVERT: H 116 TYR cc_start: 0.8949 (m-80) cc_final: 0.8640 (m-80) REVERT: H 123 MET cc_start: 0.8836 (tmm) cc_final: 0.8482 (tmm) REVERT: H 141 TYR cc_start: 0.9171 (m-80) cc_final: 0.8950 (m-10) REVERT: I 1 MET cc_start: 0.7960 (ptt) cc_final: 0.7751 (ptt) REVERT: I 3 THR cc_start: 0.9400 (m) cc_final: 0.9116 (p) REVERT: I 9 ASP cc_start: 0.8770 (t70) cc_final: 0.8559 (t70) REVERT: I 68 LEU cc_start: 0.9370 (mt) cc_final: 0.8871 (pt) REVERT: I 110 PHE cc_start: 0.2731 (m-80) cc_final: 0.2072 (m-80) REVERT: J 49 MET cc_start: 0.9193 (tpp) cc_final: 0.8779 (mmm) REVERT: K 7 PHE cc_start: 0.9113 (p90) cc_final: 0.8815 (p90) REVERT: K 22 ASP cc_start: 0.9403 (t0) cc_final: 0.8923 (p0) REVERT: K 50 LEU cc_start: 0.9685 (mt) cc_final: 0.9448 (mt) REVERT: K 75 ILE cc_start: 0.9559 (mp) cc_final: 0.9351 (mp) REVERT: K 106 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9346 (mt-10) REVERT: L 30 ILE cc_start: 0.8939 (mm) cc_final: 0.8580 (tp) REVERT: L 56 LEU cc_start: 0.8640 (mt) cc_final: 0.8120 (mt) REVERT: L 57 LEU cc_start: 0.8838 (mp) cc_final: 0.8571 (mp) REVERT: L 63 ARG cc_start: 0.8621 (mtm110) cc_final: 0.8071 (tmm-80) REVERT: L 67 PHE cc_start: 0.8907 (m-80) cc_final: 0.8636 (m-80) outliers start: 1 outliers final: 0 residues processed: 495 average time/residue: 0.2147 time to fit residues: 176.6372 Evaluate side-chains 405 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 241 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 314 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 335 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 361 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 HIS C 79 GLN E 114 ASN F 100 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 90 GLN I 108 HIS K 40 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.042174 restraints weight = 168880.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.043435 restraints weight = 96004.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.044306 restraints weight = 65567.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.044884 restraints weight = 50510.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.045293 restraints weight = 42500.877| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33690 Z= 0.120 Angle : 0.636 11.965 45876 Z= 0.322 Chirality : 0.044 0.375 5155 Planarity : 0.004 0.063 5603 Dihedral : 17.528 179.570 5255 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 0.03 % Allowed : 0.64 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3833 helix: 1.63 (0.15), residues: 1304 sheet: -0.39 (0.20), residues: 617 loop : -0.42 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 130 TYR 0.022 0.001 TYR B 797 PHE 0.026 0.002 PHE G 82 TRP 0.028 0.001 TRP B 466 HIS 0.009 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (33658) covalent geometry : angle 0.61889 / 0.32 (45831) hydrogen bonds : bond 0.03360 / 2.22 ( 1412) hydrogen bonds : angle 4.77271 / 3.32 ( 3928) metal coordination : bond 0.00835 / 0.59 ( 32) metal coordination : angle 4.70812 / 3.23 ( 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 496 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 1.318 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8705 (mtm) cc_final: 0.8410 (mtt) REVERT: A 234 MET cc_start: 0.9203 (tpp) cc_final: 0.8892 (tpp) REVERT: A 341 MET cc_start: 0.9342 (mmm) cc_final: 0.9047 (mmm) REVERT: A 437 MET cc_start: 0.9135 (ptp) cc_final: 0.8712 (mpp) REVERT: A 444 PHE cc_start: 0.9090 (t80) cc_final: 0.8728 (t80) REVERT: A 453 MET cc_start: 0.9176 (mpp) cc_final: 0.8795 (mpp) REVERT: A 455 MET cc_start: 0.8700 (ttt) cc_final: 0.8084 (ttt) REVERT: A 456 MET cc_start: 0.9208 (ttm) cc_final: 0.8567 (ttm) REVERT: A 487 MET cc_start: 0.8513 (mtp) cc_final: 0.7932 (mtp) REVERT: A 510 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8948 (mp10) REVERT: A 511 ILE cc_start: 0.9217 (mp) cc_final: 0.8872 (mp) REVERT: A 521 MET cc_start: 0.9593 (ptp) cc_final: 0.9016 (mpp) REVERT: A 605 MET cc_start: 0.9074 (tpp) cc_final: 0.8795 (tpp) REVERT: A 606 LEU cc_start: 0.9513 (tp) cc_final: 0.9192 (tp) REVERT: A 676 MET cc_start: 0.9025 (mmm) cc_final: 0.8654 (mmm) REVERT: A 731 ARG cc_start: 0.9348 (mmt180) cc_final: 0.9104 (mmp80) REVERT: A 734 GLU cc_start: 0.9305 (tt0) cc_final: 0.8615 (tm-30) REVERT: A 748 MET cc_start: 0.9478 (mtm) cc_final: 0.8926 (mtp) REVERT: A 838 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8897 (tm-30) REVERT: A 846 GLU cc_start: 0.9031 (pt0) cc_final: 0.8782 (pt0) REVERT: A 873 MET cc_start: 0.9225 (mmp) cc_final: 0.8991 (mmm) REVERT: A 874 ASP cc_start: 0.9249 (t0) cc_final: 0.8731 (t70) REVERT: A 932 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9158 (mm-30) REVERT: A 956 LEU cc_start: 0.9580 (mt) cc_final: 0.9298 (mp) REVERT: A 1019 CYS cc_start: 0.9528 (m) cc_final: 0.9192 (t) REVERT: A 1062 GLU cc_start: 0.9222 (tt0) cc_final: 0.8995 (mm-30) REVERT: A 1144 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8943 (ttpt) REVERT: A 1308 THR cc_start: 0.9278 (p) cc_final: 0.9047 (t) REVERT: A 1317 MET cc_start: 0.9415 (ptp) cc_final: 0.9150 (ptm) REVERT: A 1337 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8653 (pt0) REVERT: A 1373 ASP cc_start: 0.9276 (m-30) cc_final: 0.8790 (m-30) REVERT: A 1375 MET cc_start: 0.9420 (mmt) cc_final: 0.8943 (mmm) REVERT: A 1393 ASN cc_start: 0.8946 (p0) cc_final: 0.8505 (t0) REVERT: A 1404 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7965 (mm-30) REVERT: A 1417 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 173 MET cc_start: 0.9181 (tpp) cc_final: 0.8945 (tpt) REVERT: B 224 GLN cc_start: 0.9632 (mt0) cc_final: 0.9408 (mp10) REVERT: B 381 MET cc_start: 0.9481 (mtp) cc_final: 0.9133 (mtp) REVERT: B 521 LEU cc_start: 0.9712 (mt) cc_final: 0.9462 (mt) REVERT: B 621 GLU cc_start: 0.9250 (mp0) cc_final: 0.8983 (mp0) REVERT: B 643 ASP cc_start: 0.8645 (t0) cc_final: 0.8354 (p0) REVERT: B 698 GLU cc_start: 0.9301 (tt0) cc_final: 0.9068 (tm-30) REVERT: B 747 MET cc_start: 0.9342 (mmm) cc_final: 0.8940 (mmm) REVERT: B 762 ASN cc_start: 0.9009 (m-40) cc_final: 0.8171 (m-40) REVERT: B 775 LYS cc_start: 0.9384 (mtmt) cc_final: 0.9054 (mtmm) REVERT: B 821 GLN cc_start: 0.9081 (mp10) cc_final: 0.8110 (mp10) REVERT: B 999 MET cc_start: 0.8971 (mmt) cc_final: 0.8647 (mmt) REVERT: B 1128 LEU cc_start: 0.9279 (mt) cc_final: 0.9068 (mt) REVERT: B 1132 GLU cc_start: 0.8652 (pm20) cc_final: 0.8292 (pp20) REVERT: B 1133 MET cc_start: 0.8971 (mtp) cc_final: 0.8317 (mtp) REVERT: B 1136 ASP cc_start: 0.9257 (m-30) cc_final: 0.8597 (m-30) REVERT: B 1138 MET cc_start: 0.9411 (mmp) cc_final: 0.9148 (mmm) REVERT: B 1152 MET cc_start: 0.9112 (mmt) cc_final: 0.8897 (mmt) REVERT: B 1202 LEU cc_start: 0.9675 (tp) cc_final: 0.9439 (tp) REVERT: B 1206 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9298 (mt-10) REVERT: B 1208 MET cc_start: 0.9463 (mtt) cc_final: 0.9138 (mtp) REVERT: C 26 ASP cc_start: 0.9079 (p0) cc_final: 0.8777 (p0) REVERT: C 29 MET cc_start: 0.9450 (ttm) cc_final: 0.9120 (mtm) REVERT: C 37 MET cc_start: 0.9319 (mtp) cc_final: 0.9016 (mtp) REVERT: C 166 GLU cc_start: 0.8837 (tt0) cc_final: 0.8345 (tp30) REVERT: E 32 GLN cc_start: 0.9274 (tt0) cc_final: 0.8777 (tp-100) REVERT: E 57 MET cc_start: 0.9409 (mtm) cc_final: 0.9182 (mtp) REVERT: E 58 MET cc_start: 0.9243 (mmm) cc_final: 0.8768 (mmm) REVERT: E 74 ASP cc_start: 0.9369 (p0) cc_final: 0.9035 (p0) REVERT: E 215 MET cc_start: 0.8932 (ptt) cc_final: 0.8554 (ppp) REVERT: F 85 MET cc_start: 0.9599 (tmm) cc_final: 0.9189 (tmm) REVERT: F 88 TYR cc_start: 0.9234 (m-10) cc_final: 0.8613 (m-10) REVERT: F 99 LEU cc_start: 0.9656 (tp) cc_final: 0.9418 (tp) REVERT: F 103 MET cc_start: 0.9535 (mmp) cc_final: 0.9101 (mmm) REVERT: F 118 LEU cc_start: 0.9710 (tp) cc_final: 0.9466 (tp) REVERT: F 119 ARG cc_start: 0.9595 (tpp80) cc_final: 0.9168 (tpp80) REVERT: F 122 MET cc_start: 0.9657 (mtm) cc_final: 0.9076 (mtp) REVERT: F 123 LYS cc_start: 0.9442 (ttpp) cc_final: 0.9133 (tmmt) REVERT: F 124 GLU cc_start: 0.9249 (tp30) cc_final: 0.8868 (mm-30) REVERT: G 3 PHE cc_start: 0.9274 (m-80) cc_final: 0.8656 (m-80) REVERT: G 22 MET cc_start: 0.9197 (ptt) cc_final: 0.8401 (ptp) REVERT: G 47 CYS cc_start: 0.9321 (t) cc_final: 0.9081 (t) REVERT: G 60 ARG cc_start: 0.9408 (ttp80) cc_final: 0.8898 (ttp80) REVERT: H 22 LYS cc_start: 0.9483 (mttp) cc_final: 0.9130 (mmmm) REVERT: H 45 GLU cc_start: 0.8626 (mp0) cc_final: 0.7976 (mp0) REVERT: H 105 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8046 (tm-30) REVERT: H 116 TYR cc_start: 0.8947 (m-80) cc_final: 0.8590 (m-80) REVERT: H 123 MET cc_start: 0.8824 (tmm) cc_final: 0.8451 (tmm) REVERT: I 3 THR cc_start: 0.9406 (m) cc_final: 0.9130 (p) REVERT: I 68 LEU cc_start: 0.9343 (mt) cc_final: 0.8805 (pt) REVERT: I 110 PHE cc_start: 0.3054 (m-80) cc_final: 0.2403 (m-80) REVERT: J 60 PHE cc_start: 0.9579 (m-10) cc_final: 0.9004 (m-80) REVERT: K 22 ASP cc_start: 0.9378 (t0) cc_final: 0.8923 (p0) REVERT: K 50 LEU cc_start: 0.9684 (mt) cc_final: 0.9473 (mt) REVERT: K 98 LEU cc_start: 0.9489 (mm) cc_final: 0.9252 (mm) REVERT: L 30 ILE cc_start: 0.9007 (mm) cc_final: 0.8649 (tp) REVERT: L 56 LEU cc_start: 0.8765 (mt) cc_final: 0.8252 (mt) REVERT: L 57 LEU cc_start: 0.8839 (mp) cc_final: 0.8584 (mp) REVERT: L 63 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8049 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.2124 time to fit residues: 174.6504 Evaluate side-chains 405 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 221 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN B 433 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN E 114 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.040908 restraints weight = 174584.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.042086 restraints weight = 99657.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.042942 restraints weight = 69068.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.043511 restraints weight = 53397.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.043852 restraints weight = 44852.554| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33690 Z= 0.241 Angle : 0.703 13.442 45876 Z= 0.357 Chirality : 0.045 0.369 5155 Planarity : 0.004 0.055 5603 Dihedral : 17.590 178.234 5255 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % 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: 0.23 (0.14), residues: 3833 helix: 1.44 (0.14), residues: 1311 sheet: -0.50 (0.20), residues: 606 loop : -0.48 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 127 TYR 0.045 0.002 TYR B 275 PHE 0.045 0.002 PHE A1402 TRP 0.032 0.002 TRP B 466 HIS 0.009 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (33658) covalent geometry : angle 0.68344 / 0.36 (45831) hydrogen bonds : bond 0.03916 / 2.60 ( 1412) hydrogen bonds : angle 4.98219 / 3.47 ( 3928) metal coordination : bond 0.00945 / 0.62 ( 32) metal coordination : angle 5.35574 / 3.68 ( 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 459 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 1.337 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: 0.8714 (mtm) cc_final: 0.8415 (mtt) REVERT: A 234 MET cc_start: 0.9221 (tpp) cc_final: 0.8896 (tpp) REVERT: A 341 MET cc_start: 0.9341 (mmm) cc_final: 0.9066 (mmm) REVERT: A 437 MET cc_start: 0.9070 (ptp) cc_final: 0.8691 (mpp) REVERT: A 453 MET cc_start: 0.9196 (mpp) cc_final: 0.8883 (mpp) REVERT: A 455 MET cc_start: 0.8786 (ttt) cc_final: 0.8186 (ttt) REVERT: A 456 MET cc_start: 0.9217 (ttm) cc_final: 0.8507 (ttm) REVERT: A 487 MET cc_start: 0.8524 (mtp) cc_final: 0.7851 (mtt) REVERT: A 605 MET cc_start: 0.9011 (tpp) cc_final: 0.8732 (tpp) REVERT: A 676 MET cc_start: 0.9051 (mmm) cc_final: 0.8712 (mmm) REVERT: A 731 ARG cc_start: 0.9386 (mmt180) cc_final: 0.9101 (mmp80) REVERT: A 748 MET cc_start: 0.9472 (mtm) cc_final: 0.9008 (mtp) REVERT: A 838 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8992 (tm-30) REVERT: A 873 MET cc_start: 0.9309 (mmp) cc_final: 0.9073 (mmm) REVERT: A 874 ASP cc_start: 0.9246 (t0) cc_final: 0.8761 (t70) REVERT: A 932 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9217 (mm-30) REVERT: A 956 LEU cc_start: 0.9591 (mt) cc_final: 0.9304 (mp) REVERT: A 997 LEU cc_start: 0.9295 (mp) cc_final: 0.8697 (mt) REVERT: A 1144 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8988 (ttpt) REVERT: A 1308 THR cc_start: 0.9311 (p) cc_final: 0.9056 (t) REVERT: A 1317 MET cc_start: 0.9433 (ptp) cc_final: 0.9192 (ptm) REVERT: A 1337 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8685 (pt0) REVERT: A 1373 ASP cc_start: 0.9284 (m-30) cc_final: 0.8837 (m-30) REVERT: A 1375 MET cc_start: 0.9449 (mmt) cc_final: 0.8971 (mmm) REVERT: A 1404 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8074 (mm-30) REVERT: A 1417 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 173 MET cc_start: 0.9170 (tpp) cc_final: 0.8907 (tpt) REVERT: B 224 GLN cc_start: 0.9656 (mt0) cc_final: 0.9423 (mp10) REVERT: B 259 TYR cc_start: 0.8899 (m-80) cc_final: 0.8272 (m-80) REVERT: B 310 MET cc_start: 0.9562 (mtp) cc_final: 0.9285 (mtp) REVERT: B 381 MET cc_start: 0.9477 (mtp) cc_final: 0.9125 (mtp) REVERT: B 521 LEU cc_start: 0.9698 (mt) cc_final: 0.9418 (mt) REVERT: B 643 ASP cc_start: 0.8731 (t0) cc_final: 0.8407 (p0) REVERT: B 698 GLU cc_start: 0.9401 (tt0) cc_final: 0.9176 (tm-30) REVERT: B 747 MET cc_start: 0.9373 (mmm) cc_final: 0.8959 (mmm) REVERT: B 762 ASN cc_start: 0.9132 (m-40) cc_final: 0.8257 (m110) REVERT: B 775 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9055 (mtmt) REVERT: B 821 GLN cc_start: 0.9146 (mp10) cc_final: 0.8534 (mp10) REVERT: B 1134 GLU cc_start: 0.9436 (mp0) cc_final: 0.8971 (mp0) REVERT: B 1136 ASP cc_start: 0.9230 (m-30) cc_final: 0.8523 (m-30) REVERT: B 1138 MET cc_start: 0.9398 (mmp) cc_final: 0.9086 (mmm) REVERT: B 1152 MET cc_start: 0.9029 (mmt) cc_final: 0.8385 (mmm) REVERT: B 1202 LEU cc_start: 0.9717 (tp) cc_final: 0.9478 (tp) REVERT: B 1204 PHE cc_start: 0.9724 (m-80) cc_final: 0.9509 (m-80) REVERT: B 1206 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9334 (mt-10) REVERT: B 1208 MET cc_start: 0.9519 (mtt) cc_final: 0.8939 (mmm) REVERT: C 26 ASP cc_start: 0.9053 (p0) cc_final: 0.8744 (p0) REVERT: C 29 MET cc_start: 0.9438 (ttm) cc_final: 0.9143 (mtm) REVERT: C 37 MET cc_start: 0.9364 (mtp) cc_final: 0.9108 (mtp) REVERT: C 166 GLU cc_start: 0.8880 (tt0) cc_final: 0.8443 (tp30) REVERT: D 147 TYR cc_start: 0.7911 (t80) cc_final: 0.7707 (t80) REVERT: E 32 GLN cc_start: 0.9294 (tt0) cc_final: 0.8761 (tp-100) REVERT: E 57 MET cc_start: 0.9407 (mtm) cc_final: 0.9201 (mtp) REVERT: E 58 MET cc_start: 0.9355 (mmm) cc_final: 0.9112 (mmm) REVERT: E 215 MET cc_start: 0.8945 (ptt) cc_final: 0.8569 (ppp) REVERT: F 85 MET cc_start: 0.9606 (tmm) cc_final: 0.9159 (tmm) REVERT: F 88 TYR cc_start: 0.9337 (m-10) cc_final: 0.8742 (m-10) REVERT: F 99 LEU cc_start: 0.9678 (tp) cc_final: 0.9411 (tp) REVERT: F 103 MET cc_start: 0.9558 (mmp) cc_final: 0.9106 (mmm) REVERT: F 118 LEU cc_start: 0.9750 (tp) cc_final: 0.9523 (tp) REVERT: F 119 ARG cc_start: 0.9595 (tpp80) cc_final: 0.9256 (mmm-85) REVERT: F 122 MET cc_start: 0.9675 (mtm) cc_final: 0.9127 (mtp) REVERT: F 124 GLU cc_start: 0.9351 (tp30) cc_final: 0.8867 (mm-30) REVERT: G 3 PHE cc_start: 0.9266 (m-80) cc_final: 0.8709 (m-80) REVERT: G 22 MET cc_start: 0.9100 (ptt) cc_final: 0.8308 (ptp) REVERT: G 47 CYS cc_start: 0.9294 (t) cc_final: 0.9068 (t) REVERT: G 60 ARG cc_start: 0.9388 (ttp80) cc_final: 0.8914 (ttp80) REVERT: G 99 PHE cc_start: 0.6827 (p90) cc_final: 0.6600 (p90) REVERT: H 22 LYS cc_start: 0.9463 (mttp) cc_final: 0.9132 (mmmm) REVERT: H 45 GLU cc_start: 0.8688 (mp0) cc_final: 0.8202 (mp0) REVERT: H 105 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7995 (tm-30) REVERT: I 3 THR cc_start: 0.9415 (m) cc_final: 0.9140 (p) REVERT: I 9 ASP cc_start: 0.8771 (t70) cc_final: 0.8542 (t70) REVERT: I 27 PHE cc_start: 0.8812 (m-80) cc_final: 0.8575 (m-10) REVERT: I 68 LEU cc_start: 0.9405 (mt) cc_final: 0.8904 (pt) REVERT: I 100 PHE cc_start: 0.7565 (m-80) cc_final: 0.7361 (m-10) REVERT: I 110 PHE cc_start: 0.3038 (m-80) cc_final: 0.2450 (m-80) REVERT: J 49 MET cc_start: 0.9164 (mmm) cc_final: 0.8365 (mmm) REVERT: K 7 PHE cc_start: 0.8980 (p90) cc_final: 0.8702 (p90) REVERT: K 49 GLU cc_start: 0.9110 (tp30) cc_final: 0.8854 (tp30) REVERT: K 106 GLU cc_start: 0.9563 (mt-10) cc_final: 0.9361 (mt-10) REVERT: L 30 ILE cc_start: 0.8929 (mm) cc_final: 0.8651 (mm) REVERT: L 56 LEU cc_start: 0.8888 (mt) cc_final: 0.8341 (mt) REVERT: L 63 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8097 (tmm-80) REVERT: L 67 PHE cc_start: 0.8880 (m-80) cc_final: 0.8568 (m-80) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.2093 time to fit residues: 159.5371 Evaluate side-chains 389 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 42 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 314 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN E 114 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.041331 restraints weight = 166853.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.042513 restraints weight = 97588.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.043264 restraints weight = 67462.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.043868 restraints weight = 52854.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.044218 restraints weight = 44160.222| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33690 Z= 0.192 Angle : 0.663 13.032 45876 Z= 0.336 Chirality : 0.044 0.370 5155 Planarity : 0.004 0.053 5603 Dihedral : 17.602 178.173 5255 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % 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: 0.25 (0.14), residues: 3833 helix: 1.46 (0.14), residues: 1312 sheet: -0.46 (0.20), residues: 603 loop : -0.49 (0.15), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 56 TYR 0.026 0.001 TYR B 275 PHE 0.037 0.002 PHE A1220 TRP 0.031 0.001 TRP B 466 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (33658) covalent geometry : angle 0.64248 / 0.34 (45831) hydrogen bonds : bond 0.03578 / 2.38 ( 1412) hydrogen bonds : angle 4.92151 / 3.42 ( 3928) metal coordination : bond 0.00890 / 0.60 ( 32) metal coordination : angle 5.20523 / 3.60 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5930.67 seconds wall clock time: 103 minutes 53.97 seconds (6233.97 seconds total)