Starting phenix.real_space_refine on Thu Oct 29 21:18:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g24_50963/10_2026/9g24_50963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g24_50963/10_2026/9g24_50963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g24_50963/10_2026/9g24_50963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g24_50963/10_2026/9g24_50963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g24_50963/10_2026/9g24_50963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g24_50963/10_2026/9g24_50963.map" } resolution = 3.5 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= 0.004 sd= 0.082 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 6 6.06 5 P 74 5.49 5 Mg 1 5.21 5 S 167 5.16 5 C 21343 2.51 5 N 5926 2.21 5 O 6600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34117 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11664 Classifications: {'peptide': 1478} Link IDs: {'PCIS': 4, 'PTRANS': 55, 'TRANS': 1418} Chain breaks: 5 Chain: "B" Number of atoms: 9274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9274 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 59, 'TRANS': 1108} Chain breaks: 2 Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2461 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 19, 'TRANS': 290} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1734 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "G" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1258 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain breaks: 1 Chain: "H" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1060 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 921 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain breaks: 4 Chain: "R" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "S" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 686 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'APC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 461 SG CYS A 62 53.272 85.453 86.964 1.00 97.74 S ATOM 480 SG CYS A 65 53.270 89.200 87.813 1.00 96.17 S ATOM 535 SG CYS A 72 56.175 87.712 85.852 1.00 97.18 S ATOM 781 SG CYS A 102 82.207 64.778 124.313 1.00121.55 S ATOM 806 SG CYS A 105 81.138 67.795 126.138 1.00122.07 S ATOM 1583 SG CYS A 233 84.759 66.936 126.183 1.00122.27 S ATOM 1605 SG CYS A 236 82.213 64.869 128.229 1.00128.76 S ATOM 20293 SG CYS B1104 60.018 96.078 102.362 1.00 93.74 S ATOM 20319 SG CYS B1107 60.030 92.190 102.339 1.00 96.78 S ATOM 20466 SG CYS B1128 57.219 94.489 101.003 1.00103.90 S ATOM 20494 SG CYS B1131 57.975 93.944 104.842 1.00105.47 S ATOM 28788 SG CYS I 10 127.636 26.577 81.521 1.00113.54 S ATOM 28810 SG CYS I 13 124.105 27.216 80.168 1.00116.27 S ATOM 28930 SG CYS I 30 124.563 26.736 83.886 1.00120.90 S ATOM 28951 SG CYS I 33 125.141 23.812 81.663 1.00124.08 S ATOM 29258 SG CYS J 7 96.011 104.350 30.439 1.00 57.14 S ATOM 29281 SG CYS J 10 95.981 107.707 28.884 1.00 55.53 S ATOM 29561 SG CYS J 45 99.302 106.005 30.305 1.00 55.31 S ATOM 29567 SG CYS J 46 97.670 105.001 27.002 1.00 56.68 S ATOM 30582 SG CYS L 31 70.872 68.112 31.334 1.00 88.58 S ATOM 30602 SG CYS L 34 70.558 66.723 27.702 1.00 91.63 S ATOM 30706 SG CYS L 48 67.594 66.378 30.247 1.00 98.31 S ATOM 30729 SG CYS L 51 70.751 64.504 30.646 1.00 99.00 S Time building chain proxies: 8.49, per 1000 atoms: 0.25 Number of scatterers: 34117 At special positions: 0 Unit cell: (166.473, 168.567, 152.862, 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 6 29.99 S 167 16.00 P 74 15.00 Mg 1 11.99 O 6600 8.00 N 5926 7.00 C 21343 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 33 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7724 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 54 sheets defined 37.5% alpha, 17.4% beta 28 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.808A pdb=" N HIS A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 4.151A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 199 removed outlier: 3.564A pdb=" N SER A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 228 Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.864A pdb=" N THR A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 380 through 408 Processing helix chain 'A' and resid 412 through 439 Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 619 through 625 removed outlier: 4.428A pdb=" N ALA A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 671 through 681 removed outlier: 4.054A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.935A pdb=" N GLY A 761 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 824 Proline residue: A 803 - end of helix removed outlier: 3.701A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 4.051A pdb=" N LEU A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 834 " --> pdb=" O MET A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 834' Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 886 through 912 removed outlier: 3.640A pdb=" N GLY A 890 " --> pdb=" O ASN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.797A pdb=" N GLY A 980 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 removed outlier: 3.542A pdb=" N ALA A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1028 Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 4.771A pdb=" N SER A1061 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A1062 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A1063 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1091 through 1108 Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1177 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.512A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1259 Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 3.912A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1338 removed outlier: 4.916A pdb=" N ILE A1322 " --> pdb=" O SER A1318 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N HIS A1323 " --> pdb=" O ASN A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1486 through 1496 Processing helix chain 'A' and resid 1526 through 1531 removed outlier: 3.576A pdb=" N TRP A1530 " --> pdb=" O PHE A1526 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1526 through 1531' Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.810A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1568 removed outlier: 7.912A pdb=" N VAL A1555 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N GLU A1556 " --> pdb=" O THR A1552 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A1557 " --> pdb=" O TYR A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.860A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1603 removed outlier: 3.624A pdb=" N MET A1603 " --> pdb=" O ARG A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 4.268A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.749A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.038A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 41' Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.676A pdb=" N THR B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.850A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 59 through 69 removed outlier: 4.279A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.106A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.985A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 334 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 405 through 434 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.868A pdb=" N VAL B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.829A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.615A pdb=" N ALA B 510 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.548A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.527A pdb=" N SER B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.609A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.531A pdb=" N ILE B 681 " --> pdb=" O PRO B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.670A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.552A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.734A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.912A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 952 through 958 removed outlier: 4.496A pdb=" N SER B 956 " --> pdb=" O HIS B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.762A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.652A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1044 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1085 through 1093 Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.564A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.604A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.553A pdb=" N GLN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 39 through 44 removed outlier: 4.181A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.919A pdb=" N LYS D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 27 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.610A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.886A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 4.129A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 4.054A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 58 through 73 removed outlier: 3.643A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.862A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.700A 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 19 through 23 removed outlier: 3.940A pdb=" N VAL I 23 " --> pdb=" O PRO I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 53 removed outlier: 4.638A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.650A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.578A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 103 through 107 removed outlier: 3.853A pdb=" N ASN M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 107' Processing helix chain 'N' and resid 149 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.601A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.525A pdb=" N VAL A 362 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA4, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.669A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 590 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.328A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 721 removed outlier: 7.276A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 719 through 721 removed outlier: 7.276A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR H 115 " --> pdb=" O LYS H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 750 through 752 removed outlier: 6.268A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.547A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1026 through 1035 current: chain 'B' and resid 787 through 790 removed outlier: 7.941A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 917 through 919 removed outlier: 4.392A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 7.444A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1507 through 1508 removed outlier: 4.700A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 7.022A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1461 through 1462 removed outlier: 3.974A pdb=" N CYS A1470 " --> pdb=" O MET A1294 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A1294 " --> pdb=" O CYS A1470 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A1292 " --> pdb=" O PHE A1472 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 143 through 144 removed outlier: 5.102A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 144 removed outlier: 5.102A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR G 123 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73 removed outlier: 3.734A pdb=" N ILE B 73 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 73 removed outlier: 3.734A pdb=" N ILE B 73 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.970A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 216 Processing sheet with id=AC5, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.581A pdb=" N SER B 238 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AC7, first strand: chain 'B' and resid 502 through 503 removed outlier: 3.548A pdb=" N ASN B 543 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 552 removed outlier: 3.995A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 552 removed outlier: 3.995A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.553A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.520A pdb=" N VAL B 901 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.520A pdb=" N VAL B 901 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR L 29 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD5, first strand: chain 'B' and resid 823 through 825 Processing sheet with id=AD6, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD7, first strand: chain 'B' and resid 1098 through 1103 Processing sheet with id=AD8, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD9, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AE1, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.756A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 232 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 46 through 47 removed outlier: 6.927A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.357A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.601A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE7, first strand: chain 'E' and resid 61 through 62 removed outlier: 5.988A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.875A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AF1, first strand: chain 'G' and resid 132 through 135 removed outlier: 4.258A pdb=" N LEU G 133 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY G 135 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU G 229 " --> pdb=" O GLY G 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AF3, first strand: chain 'H' and resid 15 through 16 Processing sheet with id=AF4, first strand: chain 'H' and resid 28 through 29 removed outlier: 3.672A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AF6, first strand: chain 'K' and resid 47 through 49 removed outlier: 6.748A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 22 through 25 removed outlier: 7.175A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR M 62 " --> pdb=" O GLY M 55 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU M 53 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL N 111 " --> pdb=" O LYS N 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 74 through 79 removed outlier: 3.520A pdb=" N GLY M 79 " --> pdb=" O TRP N 54 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 81 through 82 removed outlier: 3.918A pdb=" N ILE N 82 " --> pdb=" O HIS N 85 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS N 85 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP N 86 " --> pdb=" O THR N 142 " (cutoff:3.500A) 1285 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 11.62 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.20: 2 1.20 - 1.55: 34455 1.55 - 1.90: 460 1.90 - 2.25: 1 2.25 - 2.60: 1 Bond restraints: 34919 Sorted by residual: bond pdb=" CB PRO M 94 " pdb=" CG PRO M 94 " ideal model delta sigma weight residual 1.492 2.595 -1.103 5.00e-02 4.00e+02 4.87e+02 bond pdb=" CG PRO M 94 " pdb=" CD PRO M 94 " ideal model delta sigma weight residual 1.503 0.845 0.658 3.40e-02 8.65e+02 3.74e+02 bond pdb=" C1' APC A1703 " pdb=" C2' APC A1703 " ideal model delta sigma weight residual 1.531 1.342 0.189 1.20e-02 6.94e+03 2.48e+02 bond pdb=" C1' APC A1703 " pdb=" O4' APC A1703 " ideal model delta sigma weight residual 1.416 1.606 -0.190 1.30e-02 5.92e+03 2.14e+02 bond pdb=" C4' APC A1703 " pdb=" O4' APC A1703 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.68e+02 ... (remaining 34914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 47483 21.21 - 42.43: 1 42.43 - 63.64: 0 63.64 - 84.85: 0 84.85 - 106.07: 1 Bond angle restraints: 47485 Sorted by residual: angle pdb=" CB PRO M 94 " pdb=" CG PRO M 94 " pdb=" CD PRO M 94 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO M 94 " pdb=" N PRO M 94 " pdb=" CD PRO M 94 " ideal model delta sigma weight residual 112.00 95.80 16.20 1.40e+00 5.10e-01 1.34e+02 angle pdb=" CA PRO M 94 " pdb=" CB PRO M 94 " pdb=" CG PRO M 94 " ideal model delta sigma weight residual 104.50 84.59 19.91 1.90e+00 2.77e-01 1.10e+02 angle pdb=" C5 APC A1703 " pdb=" C4 APC A1703 " pdb=" N3 APC A1703 " ideal model delta sigma weight residual 126.80 117.48 9.32 1.00e+00 1.00e+00 8.68e+01 angle pdb=" N PRO M 94 " pdb=" CA PRO M 94 " pdb=" CB PRO M 94 " ideal model delta sigma weight residual 103.36 96.27 7.09 8.80e-01 1.29e+00 6.49e+01 ... (remaining 47480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 19912 34.03 - 68.05: 1145 68.05 - 102.08: 77 102.08 - 136.10: 3 136.10 - 170.13: 3 Dihedral angle restraints: 21140 sinusoidal: 9180 harmonic: 11960 Sorted by residual: dihedral pdb=" CA ASP A 627 " pdb=" C ASP A 627 " pdb=" N PHE A 628 " pdb=" CA PHE A 628 " ideal model delta harmonic sigma weight residual 180.00 148.87 31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA PRO M 94 " pdb=" CB PRO M 94 " pdb=" CG PRO M 94 " pdb=" CD PRO M 94 " ideal model delta sinusoidal sigma weight residual 38.00 163.38 -125.38 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N GLN A 671 " pdb=" CA GLN A 671 " ideal model delta harmonic sigma weight residual 180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 21137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5050 0.095 - 0.190: 259 0.190 - 0.285: 2 0.285 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 5312 Sorted by residual: chirality pdb=" CB THR D 25 " pdb=" CA THR D 25 " pdb=" OG1 THR D 25 " pdb=" CG2 THR D 25 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C3' 3DR T 17 " pdb=" C4' 3DR T 17 " pdb=" O3' 3DR T 17 " pdb=" C2' 3DR T 17 " both_signs ideal model delta sigma weight residual False -2.70 -2.47 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C2' APC A1703 " pdb=" C1' APC A1703 " pdb=" C3' APC A1703 " pdb=" O2' APC A1703 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 5309 not shown) Planarity restraints: 5884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 487 " 0.103 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO A 488 " -0.265 5.00e-02 4.00e+02 pdb=" CA PRO A 488 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 488 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 117 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 118 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO E 118 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 118 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 600 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C GLN B 600 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN B 600 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 601 " 0.017 2.00e-02 2.50e+03 ... (remaining 5881 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 297 2.49 - 3.09: 23561 3.09 - 3.69: 53749 3.69 - 4.30: 75240 4.30 - 4.90: 125945 Nonbonded interactions: 278792 Sorted by model distance: nonbonded pdb=" NH2 ARG A 591 " pdb="MG MG A1704 " model vdw 1.883 2.250 nonbonded pdb=" OD2 ASP A 629 " pdb=" O3' G R 12 " model vdw 1.897 3.040 nonbonded pdb=" OD1 ASP A 631 " pdb=" O3' G R 12 " model vdw 1.966 3.040 nonbonded pdb=" OG SER L 36 " pdb="ZN ZN L3001 " model vdw 2.052 2.230 nonbonded pdb=" OG SER A1137 " pdb=" OH TYR A1174 " model vdw 2.139 3.040 ... (remaining 278787 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 45.290 Find NCS groups from input model: 0.180 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.008 1.103 34943 Z= 0.303 Angle : 0.814 106.068 47518 Z= 0.404 Chirality : 0.043 0.474 5312 Planarity : 0.005 0.153 5884 Dihedral : 19.389 170.131 13416 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.27 % Allowed : 33.93 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 4058 helix: 1.08 (0.15), residues: 1273 sheet: -1.32 (0.20), residues: 635 loop : -0.66 (0.14), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 591 TYR 0.022 0.001 TYR A 618 PHE 0.019 0.001 PHE A 223 TRP 0.047 0.001 TRP E 13 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.30 (34919) covalent geometry : angle 0.80678 / 0.40 (47485) hydrogen bonds : bond 0.17716 / 11.55 ( 1309) hydrogen bonds : angle 7.18223 / 5.07 ( 3668) metal coordination : bond 0.00599 / 0.34 ( 24) metal coordination : angle 4.26562 / 2.81 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 452 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 81 MET cc_start: 0.6850 (ttp) cc_final: 0.6633 (ttp) outliers start: 10 outliers final: 7 residues processed: 457 average time/residue: 0.1986 time to fit residues: 151.5802 Evaluate side-chains 451 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 444 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1533 GLU Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 93 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 235 ASN A 322 ASN A 344 ASN A 470 HIS A 525 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN A 625 ASN A 738 ASN A 748 ASN A 767 ASN A 880 GLN A 942 GLN A1151 ASN A1250 GLN A1314 GLN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 HIS A1514 ASN B 27 ASN B 231 HIS B 243 GLN B 251 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 398 GLN B 400 GLN B 469 ASN B 636 GLN B 673 ASN B 683 ASN B 715 ASN B 735 HIS B 823 GLN B 923 GLN B 950 ASN B1045 GLN B1165 ASN C 297 HIS C 301 ASN D 88 GLN E 179 GLN F 78 GLN G 150 HIS I 41 GLN K 64 GLN K 102 ASN L 53 HIS L 66 GLN ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.147898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111551 restraints weight = 57347.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114401 restraints weight = 30862.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116275 restraints weight = 21087.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117441 restraints weight = 16763.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118089 restraints weight = 14656.692| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.076 34943 Z= 0.279 Angle : 0.835 106.100 47518 Z= 0.386 Chirality : 0.046 0.253 5312 Planarity : 0.005 0.096 5884 Dihedral : 13.068 171.570 5318 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.96 % Allowed : 31.12 % Favored : 64.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 4058 helix: 1.02 (0.15), residues: 1284 sheet: -1.63 (0.20), residues: 641 loop : -0.66 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1021 TYR 0.015 0.002 TYR A 188 PHE 0.024 0.002 PHE A 223 TRP 0.015 0.001 TRP B 143 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.28 (34919) covalent geometry : angle 0.82048 / 0.39 (47485) hydrogen bonds : bond 0.05437 / 3.56 ( 1309) hydrogen bonds : angle 5.84625 / 4.14 ( 3668) metal coordination : bond 0.01058 / 0.69 ( 24) metal coordination : angle 5.89619 / 3.74 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 453 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6031 (OUTLIER) cc_final: 0.5707 (t) REVERT: A 232 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4560 (tttt) REVERT: A 265 ARG cc_start: 0.7545 (mmt180) cc_final: 0.6735 (mmt-90) REVERT: A 549 MET cc_start: 0.6488 (mtp) cc_final: 0.6199 (mtp) REVERT: A 654 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8041 (p0) REVERT: A 1221 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8102 (tpt-90) REVERT: B 242 ASP cc_start: 0.8070 (p0) cc_final: 0.7771 (p0) REVERT: B 414 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6996 (ttpp) REVERT: B 555 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8137 (tp40) REVERT: B 668 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: G 71 MET cc_start: 0.7702 (mtm) cc_final: 0.7452 (mtt) REVERT: H 25 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.6962 (ttt-90) REVERT: I 34 LYS cc_start: 0.7455 (mtmm) cc_final: 0.7052 (mptt) REVERT: M 76 TYR cc_start: 0.7556 (m-80) cc_final: 0.6861 (m-80) REVERT: M 92 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5836 (mptt) REVERT: N 52 GLN cc_start: 0.5138 (pm20) cc_final: 0.4800 (pm20) outliers start: 144 outliers final: 79 residues processed: 549 average time/residue: 0.2057 time to fit residues: 186.5621 Evaluate side-chains 529 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 441 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1608 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [174, 128, 341, 328, 201, 376, 213, 149, 183, 265, 338] chunk 174 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 341 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 376 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS A 625 ASN A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN B 27 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN I 41 GLN L 53 HIS ** M 57 ASN ** 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 = 0.4034 r_free = 0.4034 target = 0.149767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112940 restraints weight = 57405.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115890 restraints weight = 30862.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117803 restraints weight = 21048.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118941 restraints weight = 16766.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119547 restraints weight = 14705.188| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.077 34943 Z= 0.209 Angle : 0.767 103.536 47518 Z= 0.350 Chirality : 0.043 0.291 5312 Planarity : 0.004 0.069 5884 Dihedral : 12.953 172.299 5305 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.04 % Allowed : 30.93 % Favored : 65.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 4058 helix: 1.16 (0.15), residues: 1285 sheet: -1.57 (0.20), residues: 612 loop : -0.66 (0.14), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1559 TYR 0.013 0.001 TYR A1302 PHE 0.022 0.001 PHE A 223 TRP 0.013 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.21 (34919) covalent geometry : angle 0.75848 / 0.35 (47485) hydrogen bonds : bond 0.04312 / 2.84 ( 1309) hydrogen bonds : angle 5.36569 / 3.78 ( 3668) metal coordination : bond 0.00664 / 0.44 ( 24) metal coordination : angle 4.47885 / 2.93 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 483 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.4887 (OUTLIER) cc_final: 0.4470 (tttt) REVERT: A 265 ARG cc_start: 0.7601 (mmt180) cc_final: 0.7183 (mmt180) REVERT: A 321 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6939 (tttp) REVERT: A 475 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.6398 (mtt-85) REVERT: A 549 MET cc_start: 0.6483 (mtp) cc_final: 0.6122 (mtp) REVERT: A 1124 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7532 (mm) REVERT: A 1221 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8105 (tpt-90) REVERT: B 237 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8159 (ttt-90) REVERT: B 242 ASP cc_start: 0.8000 (p0) cc_final: 0.7767 (p0) REVERT: B 277 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 555 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8108 (tp40) REVERT: B 668 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: B 821 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 851 TYR cc_start: 0.8201 (t80) cc_final: 0.7692 (t80) REVERT: D 29 GLN cc_start: 0.6538 (mp10) cc_final: 0.6185 (mp10) REVERT: G 71 MET cc_start: 0.7519 (mtm) cc_final: 0.7286 (mtt) REVERT: I 34 LYS cc_start: 0.7370 (mtmm) cc_final: 0.6897 (mptt) REVERT: L 67 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6615 (m-80) REVERT: M 92 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5195 (tttt) REVERT: N 52 GLN cc_start: 0.5111 (pm20) cc_final: 0.4720 (pm20) outliers start: 147 outliers final: 83 residues processed: 586 average time/residue: 0.2007 time to fit residues: 195.7441 Evaluate side-chains 540 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 445 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [211, 152, 12, 60, 138, 407, 207, 353, 183, 148, 49] chunk 211 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 407 optimal weight: 50.0000 chunk 207 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 923 GLN ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.148565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112287 restraints weight = 56784.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115159 restraints weight = 30518.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117045 restraints weight = 20800.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118210 restraints weight = 16535.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118849 restraints weight = 14461.820| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.097 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.32 % Allowed : 31.15 % Favored : 64.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79036 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33150 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67142 / 3.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 447 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5683 (t) REVERT: A 232 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4644 (tttt) REVERT: A 265 ARG cc_start: 0.7549 (mmt180) cc_final: 0.7205 (mmt180) REVERT: A 321 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6990 (tttp) REVERT: A 475 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6471 (mtt-85) REVERT: A 549 MET cc_start: 0.6527 (mtp) cc_final: 0.6105 (mtp) REVERT: A 1124 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 1221 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8030 (tpt-90) REVERT: A 1227 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.6088 (mmm) REVERT: B 242 ASP cc_start: 0.8094 (p0) cc_final: 0.7880 (p0) REVERT: B 555 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8127 (tp40) REVERT: B 668 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: B 821 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8009 (mp) REVERT: B 851 TYR cc_start: 0.8218 (t80) cc_final: 0.7709 (t80) REVERT: C 71 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7542 (mtp) REVERT: G 71 MET cc_start: 0.7561 (mtm) cc_final: 0.7333 (mtt) REVERT: I 34 LYS cc_start: 0.7391 (mtmm) cc_final: 0.6928 (mptt) REVERT: L 67 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: M 92 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5220 (tttt) outliers start: 157 outliers final: 118 residues processed: 552 average time/residue: 0.1949 time to fit residues: 180.1994 Evaluate side-chains 564 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 433 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [371, 120, 170, 355, 21, 400, 91, 116, 406, 389, 319] chunk 371 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 400 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 406 optimal weight: 40.0000 chunk 389 optimal weight: 20.0000 chunk 319 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 923 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112254 restraints weight = 57126.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115115 restraints weight = 30597.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117000 restraints weight = 20831.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118129 restraints weight = 16533.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118807 restraints weight = 14485.919| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.68 % Allowed : 31.73 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 434 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5683 (t) REVERT: A 232 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4639 (tttt) REVERT: A 265 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7203 (mmt180) REVERT: A 321 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6987 (tttp) REVERT: A 475 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6472 (mtt-85) REVERT: A 549 MET cc_start: 0.6524 (mtp) cc_final: 0.6103 (mtp) REVERT: A 1124 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 1221 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8028 (tpt-90) REVERT: A 1227 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.6087 (mmm) REVERT: B 242 ASP cc_start: 0.8091 (p0) cc_final: 0.7878 (p0) REVERT: B 555 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: B 668 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: B 821 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 851 TYR cc_start: 0.8216 (t80) cc_final: 0.7709 (t80) REVERT: C 71 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: G 71 MET cc_start: 0.7554 (mtm) cc_final: 0.7327 (mtt) REVERT: I 34 LYS cc_start: 0.7389 (mtmm) cc_final: 0.6928 (mptt) REVERT: L 67 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: M 92 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5221 (tttt) outliers start: 134 outliers final: 119 residues processed: 521 average time/residue: 0.1987 time to fit residues: 173.9983 Evaluate side-chains 566 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 434 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [317, 247, 316, 185, 326, 74, 266, 235, 277, 282, 143] chunk 317 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112274 restraints weight = 56914.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115142 restraints weight = 30506.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116989 restraints weight = 20765.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118129 restraints weight = 16527.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118705 restraints weight = 14483.933| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.66 % Allowed : 31.76 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 434 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5683 (t) REVERT: A 232 LYS cc_start: 0.5057 (OUTLIER) cc_final: 0.4634 (tttt) REVERT: A 265 ARG cc_start: 0.7550 (mmt180) cc_final: 0.7206 (mmt180) REVERT: A 321 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6987 (tttp) REVERT: A 475 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6470 (mtt-85) REVERT: A 549 MET cc_start: 0.6528 (mtp) cc_final: 0.6106 (mtp) REVERT: A 1124 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7553 (mm) REVERT: A 1221 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8029 (tpt-90) REVERT: A 1227 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6089 (mmm) REVERT: B 242 ASP cc_start: 0.8091 (p0) cc_final: 0.7878 (p0) REVERT: B 555 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8127 (tp40) REVERT: B 668 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: B 821 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 851 TYR cc_start: 0.8216 (t80) cc_final: 0.7708 (t80) REVERT: C 71 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: G 71 MET cc_start: 0.7548 (mtm) cc_final: 0.7321 (mtt) REVERT: I 34 LYS cc_start: 0.7391 (mtmm) cc_final: 0.6927 (mptt) REVERT: L 67 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: M 92 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.5213 (tttt) outliers start: 133 outliers final: 119 residues processed: 521 average time/residue: 0.1970 time to fit residues: 172.9321 Evaluate side-chains 566 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 434 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [295, 170, 159, 246, 280, 89, 219, 346, 86, 316, 15] chunk 295 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 346 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112250 restraints weight = 56970.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115138 restraints weight = 30584.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117012 restraints weight = 20786.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118101 restraints weight = 16523.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118829 restraints weight = 14496.868| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.68 % Allowed : 31.73 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 434 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6048 (OUTLIER) cc_final: 0.5685 (t) REVERT: A 232 LYS cc_start: 0.5074 (OUTLIER) cc_final: 0.4647 (tttt) REVERT: A 265 ARG cc_start: 0.7545 (mmt180) cc_final: 0.7203 (mmt180) REVERT: A 321 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6996 (tttp) REVERT: A 475 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6472 (mtt-85) REVERT: A 549 MET cc_start: 0.6526 (mtp) cc_final: 0.6102 (mtp) REVERT: A 1124 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7552 (mm) REVERT: A 1221 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8029 (tpt-90) REVERT: A 1227 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.6085 (mmm) REVERT: B 242 ASP cc_start: 0.8093 (p0) cc_final: 0.7878 (p0) REVERT: B 555 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8127 (tp40) REVERT: B 668 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: B 821 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8005 (mp) REVERT: B 851 TYR cc_start: 0.8214 (t80) cc_final: 0.7707 (t80) REVERT: C 71 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: G 71 MET cc_start: 0.7563 (mtm) cc_final: 0.7334 (mtt) REVERT: I 34 LYS cc_start: 0.7387 (mtmm) cc_final: 0.6928 (mptt) REVERT: L 67 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: M 92 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.5232 (tttt) outliers start: 134 outliers final: 119 residues processed: 521 average time/residue: 0.1994 time to fit residues: 174.7638 Evaluate side-chains 566 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 434 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [325, 59, 123, 126, 15, 81, 342, 133, 121, 49, 404] chunk 325 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 404 optimal weight: 50.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112265 restraints weight = 57014.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115139 restraints weight = 30545.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116993 restraints weight = 20767.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118125 restraints weight = 16526.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118788 restraints weight = 14485.260| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.66 % Allowed : 31.76 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 434 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5683 (t) REVERT: A 232 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4640 (tttt) REVERT: A 265 ARG cc_start: 0.7548 (mmt180) cc_final: 0.7203 (mmt180) REVERT: A 321 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6988 (tttp) REVERT: A 475 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6473 (mtt-85) REVERT: A 549 MET cc_start: 0.6524 (mtp) cc_final: 0.6103 (mtp) REVERT: A 1124 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 1221 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8028 (tpt-90) REVERT: A 1227 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.6086 (mmm) REVERT: B 242 ASP cc_start: 0.8091 (p0) cc_final: 0.7878 (p0) REVERT: B 555 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: B 668 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: B 821 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 851 TYR cc_start: 0.8216 (t80) cc_final: 0.7708 (t80) REVERT: C 71 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7542 (mtp) REVERT: G 71 MET cc_start: 0.7556 (mtm) cc_final: 0.7328 (mtt) REVERT: I 34 LYS cc_start: 0.7389 (mtmm) cc_final: 0.6928 (mptt) REVERT: L 67 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: M 92 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5221 (tttt) outliers start: 133 outliers final: 119 residues processed: 521 average time/residue: 0.2002 time to fit residues: 175.0497 Evaluate side-chains 566 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 434 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [260, 194, 211, 241, 325, 223, 43, 304, 161, 353, 270] chunk 260 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 325 optimal weight: 0.7980 chunk 223 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112261 restraints weight = 56727.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115143 restraints weight = 30505.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116979 restraints weight = 20761.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118135 restraints weight = 16559.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118820 restraints weight = 14483.180| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.68 % Allowed : 31.73 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 434 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5685 (t) REVERT: A 232 LYS cc_start: 0.5068 (OUTLIER) cc_final: 0.4643 (tttt) REVERT: A 265 ARG cc_start: 0.7546 (mmt180) cc_final: 0.7202 (mmt180) REVERT: A 321 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6991 (tttp) REVERT: A 475 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6471 (mtt-85) REVERT: A 549 MET cc_start: 0.6526 (mtp) cc_final: 0.6102 (mtp) REVERT: A 1124 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7552 (mm) REVERT: A 1221 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8028 (tpt-90) REVERT: A 1227 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.6086 (mmm) REVERT: B 242 ASP cc_start: 0.8092 (p0) cc_final: 0.7879 (p0) REVERT: B 555 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: B 668 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: B 821 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 851 TYR cc_start: 0.8214 (t80) cc_final: 0.7707 (t80) REVERT: C 71 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: G 71 MET cc_start: 0.7562 (mtm) cc_final: 0.7332 (mtt) REVERT: I 34 LYS cc_start: 0.7389 (mtmm) cc_final: 0.6928 (mptt) REVERT: L 67 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: M 92 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5226 (tttt) outliers start: 134 outliers final: 119 residues processed: 521 average time/residue: 0.2063 time to fit residues: 179.6038 Evaluate side-chains 566 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 434 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [289, 408, 288, 130, 70, 239, 407, 378, 404, 174, 397] chunk 289 optimal weight: 1.9990 chunk 408 optimal weight: 50.0000 chunk 288 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 407 optimal weight: 50.0000 chunk 378 optimal weight: 0.6980 chunk 404 optimal weight: 50.0000 chunk 174 optimal weight: 4.9990 chunk 397 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112209 restraints weight = 56977.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115093 restraints weight = 30616.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116961 restraints weight = 20832.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118097 restraints weight = 16578.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118809 restraints weight = 14524.983| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.66 % Allowed : 31.76 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 434 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5686 (t) REVERT: A 232 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.4646 (tttt) REVERT: A 265 ARG cc_start: 0.7545 (mmt180) cc_final: 0.7202 (mmt180) REVERT: A 321 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6997 (tttp) REVERT: A 475 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6472 (mtt-85) REVERT: A 549 MET cc_start: 0.6524 (mtp) cc_final: 0.6101 (mtp) REVERT: A 1124 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7553 (mm) REVERT: A 1221 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8028 (tpt-90) REVERT: A 1227 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.6085 (mmm) REVERT: B 242 ASP cc_start: 0.8091 (p0) cc_final: 0.7878 (p0) REVERT: B 555 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8126 (tp40) REVERT: B 668 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: B 821 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8006 (mp) REVERT: B 851 TYR cc_start: 0.8214 (t80) cc_final: 0.7707 (t80) REVERT: C 71 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7542 (mtp) REVERT: G 71 MET cc_start: 0.7564 (mtm) cc_final: 0.7333 (mtt) REVERT: I 34 LYS cc_start: 0.7388 (mtmm) cc_final: 0.6928 (mptt) REVERT: L 67 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: M 92 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5233 (tttt) outliers start: 133 outliers final: 119 residues processed: 521 average time/residue: 0.1972 time to fit residues: 172.9848 Evaluate side-chains 566 residues out of total 3637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 434 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: [392, 70, 196, 175, 72, 367, 403, 222, 8, 78, 251] chunk 392 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 403 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 251 optimal weight: 0.3980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112267 restraints weight = 56788.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115146 restraints weight = 30516.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117017 restraints weight = 20766.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118140 restraints weight = 16510.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118834 restraints weight = 14472.191| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.089 34943 Z= 0.248 Angle : 0.800 106.100 47518 Z= 0.364 Chirality : 0.044 0.288 5312 Planarity : 0.004 0.066 5884 Dihedral : 12.956 172.537 5305 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.68 % Allowed : 31.73 % Favored : 64.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.62 % 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: -0.41 (0.13), residues: 4058 helix: 1.13 (0.15), residues: 1284 sheet: -1.58 (0.20), residues: 610 loop : -0.69 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.028 0.001 TYR B1032 PHE 0.037 0.001 PHE A 223 TRP 0.014 0.001 TRP B 143 HIS 0.013 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.25 (34919) covalent geometry : angle 0.79034 / 0.36 (47485) hydrogen bonds : bond 0.04324 / 2.83 ( 1309) hydrogen bonds : angle 5.33149 / 3.76 ( 3668) metal coordination : bond 0.00763 / 0.53 ( 24) metal coordination : angle 4.67141 / 3.02 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6664.53 seconds wall clock time: 115 minutes 38.47 seconds (6938.47 seconds total)