Starting phenix.real_space_refine on Tue Sep 15 02:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o4l_12722/09_2026/7o4l_12722.map" } resolution = 3.4 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= 0.052 sd= 1.010 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 11 6.06 5 P 22 5.49 5 Mg 1 5.21 5 S 210 5.16 5 Be 1 3.05 5 C 22270 2.51 5 N 6004 2.21 5 O 6633 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35159 Number of models: 1 Model: "" Number of chains: 25 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4206 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 502} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2946 Classifications: {'peptide': 374} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 352} Chain breaks: 2 Chain: "7" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4881 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 23, 'TRANS': 583} Chain breaks: 1 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1752 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 15, 'TRANS': 211} Chain breaks: 13 Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 644 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "D" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1296 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 2 Chain: "F" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 454 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain breaks: 3 Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "N" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2521 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 3 Chain: "X" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1094 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain breaks: 1 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" 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 938 SG CYS 0 115 53.305 87.610 111.138 1.00 63.26 S ATOM 1265 SG CYS 0 156 48.122 87.031 115.179 1.00 77.00 S ATOM 1080 SG CYS 0 133 50.264 92.885 113.038 1.00 69.84 S ATOM 1566 SG CYS 0 191 53.156 89.858 117.401 1.00 64.35 S ATOM 13933 SG CYS 3 13 37.976 118.384 65.689 1.00104.51 S ATOM 13954 SG CYS 3 16 39.251 118.003 62.130 1.00101.65 S ATOM 14149 SG CYS 3 39 40.467 120.890 64.340 1.00103.25 S ATOM 14170 SG CYS 3 42 36.954 120.939 63.040 1.00105.49 S ATOM 14102 SG CYS 3 34 30.720 122.926 75.103 1.00109.81 S ATOM 14260 SG CYS 3 54 30.221 122.083 71.321 1.00113.01 S ATOM 14298 SG CYS 3 59 27.223 121.640 73.766 1.00112.15 S ATOM 16962 SG CYS 4 289 103.510 47.782 132.190 1.00 69.24 S ATOM 16981 SG CYS 4 292 106.054 49.896 133.735 1.00 69.60 S ATOM 17073 SG CYS 4 305 103.947 47.292 135.863 1.00 83.87 S ATOM 17091 SG CYS 4 308 102.428 50.451 134.880 1.00 80.35 S ATOM 19910 SG CYS 6 349 106.712 31.471 118.303 1.00 70.67 S ATOM 19931 SG CYS 6 352 104.837 29.075 115.914 1.00 84.21 S ATOM 20010 SG CYS 6 363 105.159 32.686 115.060 1.00 70.40 S ATOM 20029 SG CYS 6 366 103.050 31.818 118.074 1.00 79.85 S ATOM 20331 SG CYS 6 403 133.275 66.879 130.651 1.00 79.50 S ATOM 20354 SG CYS 6 406 135.029 65.673 127.494 1.00 65.11 S ATOM 20548 SG CYS 6 437 132.463 68.433 127.253 1.00 76.82 S ATOM 20569 SG CYS 6 440 131.314 64.916 128.060 1.00 68.36 S ATOM 20481 SG CYS 6 429 123.018 64.588 136.919 1.00 87.01 S ATOM 20504 SG CYS 6 432 126.218 63.322 138.560 1.00 82.85 S ATOM 20662 SG CYS 6 451 125.519 62.371 135.001 1.00 65.89 S ATOM 20679 SG CYS 6 454 123.280 60.950 137.738 1.00 71.51 S ATOM 19809 SG CYS 6 336 110.717 32.383 104.613 1.00 94.03 S ATOM 19821 SG CYS 6 338 109.539 35.166 107.006 1.00 85.00 S ATOM 19969 SG CYS 6 357 113.247 34.670 106.257 1.00 76.59 S ATOM 26068 SG CYS A 107 77.693 113.377 39.038 1.00 94.87 S ATOM 26092 SG CYS A 110 76.676 114.657 42.418 1.00 88.57 S ATOM 26173 SG CYS A 148 80.347 113.702 41.735 1.00 93.73 S ATOM 26214 SG CYS A 167 77.646 110.995 41.943 1.00 95.42 S ATOM 25856 SG CYS A 67 39.135 138.222 24.376 1.00 62.24 S ATOM 25878 SG CYS A 70 39.568 141.735 25.846 1.00 55.94 S ATOM 25911 SG CYS A 77 41.887 140.546 23.035 1.00 65.22 S ATOM 27520 SG CYS B1163 51.902 142.987 36.674 1.00 51.22 S ATOM 27538 SG CYS B1166 53.454 140.073 34.647 1.00 50.73 S ATOM 27663 SG CYS B1182 49.734 140.166 35.405 1.00 41.66 S ATOM 27682 SG CYS B1185 52.317 139.483 38.143 1.00 43.23 S ATOM 32503 SG CYS W 124 25.224 134.963 33.154 1.00 87.67 S ATOM 32524 SG CYS W 127 28.579 134.255 31.645 1.00 88.86 S ATOM 32709 SG CYS W 149 27.645 137.830 32.704 1.00 77.79 S ATOM 32729 SG CYS W 152 26.054 136.210 29.624 1.00 80.54 S Time building chain proxies: 6.92, per 1000 atoms: 0.20 Number of scatterers: 35159 At special positions: 0 Unit cell: (193.2, 198.45, 166.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 11 29.99 Fe 4 26.01 S 210 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 6633 8.00 N 6004 7.00 C 22270 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 57 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 36 sheets defined 51.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 Processing helix chain '0' and resid 48 through 63 Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 125 through 138 Processing helix chain '0' and resid 139 through 148 Processing helix chain '0' and resid 156 through 165 removed outlier: 3.857A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE 0 165 " --> pdb=" O ASN 0 161 " (cutoff:3.500A) Processing helix chain '0' and resid 166 through 170 Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 191 through 199 Processing helix chain '0' and resid 211 through 213 No H-bonds generated for 'chain '0' and resid 211 through 213' Processing helix chain '0' and resid 215 through 218 Processing helix chain '0' and resid 219 through 224 removed outlier: 3.600A pdb=" N ASN 0 224 " --> pdb=" O GLU 0 220 " (cutoff:3.500A) Processing helix chain '0' and resid 239 through 248 removed outlier: 3.760A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 278 Processing helix chain '0' and resid 279 through 292 removed outlier: 3.637A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 Processing helix chain '0' and resid 312 through 316 Processing helix chain '0' and resid 327 through 346 Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 376 removed outlier: 3.777A pdb=" N LEU 0 374 " --> pdb=" O GLU 0 370 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) Processing helix chain '0' and resid 376 through 389 Processing helix chain '0' and resid 396 through 412 removed outlier: 3.628A pdb=" N LYS 0 400 " --> pdb=" O PHE 0 396 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE 0 402 " --> pdb=" O ALA 0 398 " (cutoff:3.500A) Processing helix chain '0' and resid 446 through 453 Processing helix chain '0' and resid 467 through 473 removed outlier: 3.686A pdb=" N ARG 0 471 " --> pdb=" O ASP 0 467 " (cutoff:3.500A) Processing helix chain '0' and resid 509 through 513 removed outlier: 3.576A pdb=" N ARG 0 513 " --> pdb=" O PHE 0 510 " (cutoff:3.500A) Processing helix chain '0' and resid 515 through 533 Processing helix chain '0' and resid 543 through 558 Processing helix chain '0' and resid 558 through 567 removed outlier: 3.672A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 Processing helix chain '0' and resid 632 through 647 Processing helix chain '0' and resid 649 through 668 removed outlier: 3.602A pdb=" N CYS 0 665 " --> pdb=" O HIS 0 661 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 693 removed outlier: 3.718A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 694 through 701 removed outlier: 3.659A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 703 through 707 removed outlier: 4.020A pdb=" N ASN 0 707 " --> pdb=" O ALA 0 704 " (cutoff:3.500A) Processing helix chain '0' and resid 710 through 725 Processing helix chain '0' and resid 729 through 734 removed outlier: 3.836A pdb=" N GLN 0 733 " --> pdb=" O ASP 0 729 " (cutoff:3.500A) Processing helix chain '0' and resid 740 through 752 Processing helix chain '1' and resid 93 through 121 Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 177 through 188 Processing helix chain '1' and resid 189 through 200 Processing helix chain '1' and resid 205 through 212 removed outlier: 3.744A pdb=" N TRP 1 210 " --> pdb=" O PRO 1 206 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER 1 211 " --> pdb=" O SER 1 207 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 213 through 223 Processing helix chain '1' and resid 232 through 237 removed outlier: 3.662A pdb=" N THR 1 236 " --> pdb=" O ASN 1 232 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE 1 237 " --> pdb=" O VAL 1 233 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 232 through 237' Processing helix chain '1' and resid 253 through 263 Processing helix chain '1' and resid 263 through 274 removed outlier: 3.654A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN 1 273 " --> pdb=" O ALA 1 269 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 289 removed outlier: 3.636A pdb=" N PHE 1 283 " --> pdb=" O LYS 1 279 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP 1 284 " --> pdb=" O GLU 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 290 through 297 removed outlier: 3.708A pdb=" N ARG 1 294 " --> pdb=" O SER 1 290 " (cutoff:3.500A) Processing helix chain '1' and resid 308 through 313 removed outlier: 3.836A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) Processing helix chain '1' and resid 314 through 330 Processing helix chain '1' and resid 339 through 345 Processing helix chain '1' and resid 355 through 359 Processing helix chain '1' and resid 370 through 390 removed outlier: 3.767A pdb=" N ILE 1 374 " --> pdb=" O GLY 1 370 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS 1 390 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 420 removed outlier: 3.707A pdb=" N GLU 1 418 " --> pdb=" O ASP 1 414 " (cutoff:3.500A) Processing helix chain '1' and resid 465 through 483 Processing helix chain '1' and resid 486 through 490 Processing helix chain '1' and resid 492 through 515 removed outlier: 3.528A pdb=" N GLN 1 513 " --> pdb=" O ILE 1 509 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 569 Processing helix chain '1' and resid 570 through 571 No H-bonds generated for 'chain '1' and resid 570 through 571' Processing helix chain '1' and resid 572 through 573 No H-bonds generated for 'chain '1' and resid 572 through 573' Processing helix chain '1' and resid 574 through 604 removed outlier: 4.537A pdb=" N THR 1 578 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 1 581 " --> pdb=" O SER 1 577 " (cutoff:3.500A) Processing helix chain '1' and resid 608 through 639 Proline residue: 1 618 - end of helix Processing helix chain '2' and resid 6 through 17 removed outlier: 4.235A pdb=" N THR 2 11 " --> pdb=" O LYS 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 26 Processing helix chain '2' and resid 28 through 39 removed outlier: 3.739A pdb=" N LEU 2 39 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 52 removed outlier: 4.138A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 66 removed outlier: 3.662A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 84 Processing helix chain '2' and resid 101 through 113 Processing helix chain '2' and resid 134 through 152 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 194 Processing helix chain '2' and resid 195 through 211 Processing helix chain '2' and resid 217 through 231 removed outlier: 3.672A pdb=" N ALA 2 230 " --> pdb=" O PHE 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 257 Processing helix chain '2' and resid 272 through 280 removed outlier: 3.558A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER 2 280 " --> pdb=" O LEU 2 276 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 362 removed outlier: 3.535A pdb=" N ILE 2 357 " --> pdb=" O SER 2 353 " (cutoff:3.500A) Processing helix chain '2' and resid 379 through 390 Processing helix chain '2' and resid 392 through 403 Processing helix chain '2' and resid 405 through 423 Processing helix chain '2' and resid 434 through 449 removed outlier: 3.507A pdb=" N VAL 2 438 " --> pdb=" O PRO 2 434 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 2 448 " --> pdb=" O TRP 2 444 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP 2 449 " --> pdb=" O GLN 2 445 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 478 Processing helix chain '2' and resid 497 through 507 Processing helix chain '3' and resid 40 through 48 removed outlier: 3.574A pdb=" N SER 3 48 " --> pdb=" O ASP 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 75 through 92 Processing helix chain '3' and resid 96 through 100 Processing helix chain '3' and resid 102 through 123 Processing helix chain '3' and resid 125 through 139 Processing helix chain '4' and resid 33 through 44 Processing helix chain '4' and resid 49 through 68 removed outlier: 3.871A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 115 through 139 removed outlier: 3.858A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 189 through 191 No H-bonds generated for 'chain '4' and resid 189 through 191' Processing helix chain '4' and resid 192 through 206 removed outlier: 3.520A pdb=" N ILE 4 200 " --> pdb=" O ILE 4 196 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 231 removed outlier: 3.741A pdb=" N GLN 4 226 " --> pdb=" O THR 4 222 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR 4 231 " --> pdb=" O THR 4 227 " (cutoff:3.500A) Processing helix chain '4' and resid 243 through 251 removed outlier: 3.740A pdb=" N TYR 4 247 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 259 Processing helix chain '4' and resid 300 through 304 removed outlier: 4.006A pdb=" N LYS 4 304 " --> pdb=" O PRO 4 301 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 322 Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 46 through 58 Processing helix chain '5' and resid 59 through 62 Processing helix chain '6' and resid 74 through 79 removed outlier: 4.052A pdb=" N ASP 6 78 " --> pdb=" O TYR 6 74 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 74 through 79' Processing helix chain '6' and resid 82 through 87 removed outlier: 4.066A pdb=" N LEU 6 86 " --> pdb=" O ARG 6 82 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL 6 87 " --> pdb=" O SER 6 83 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 82 through 87' Processing helix chain '6' and resid 97 through 114 removed outlier: 3.797A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN 6 114 " --> pdb=" O THR 6 110 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 Processing helix chain '6' and resid 144 through 164 Processing helix chain '6' and resid 188 through 200 removed outlier: 3.682A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 Processing helix chain '6' and resid 246 through 258 removed outlier: 3.899A pdb=" N THR 6 250 " --> pdb=" O ASP 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 304 removed outlier: 3.587A pdb=" N LEU 6 297 " --> pdb=" O ASP 6 293 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 6 298 " --> pdb=" O GLU 6 294 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) Processing helix chain '6' and resid 372 through 379 removed outlier: 3.673A pdb=" N LEU 6 376 " --> pdb=" O LEU 6 372 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) Processing helix chain '6' and resid 379 through 384 removed outlier: 3.833A pdb=" N LEU 6 383 " --> pdb=" O SER 6 379 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 447 removed outlier: 3.505A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 457 Processing helix chain '7' and resid 107 through 113 removed outlier: 4.431A pdb=" N GLY 7 111 " --> pdb=" O SER 7 108 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 161 removed outlier: 3.580A pdb=" N ALA 7 153 " --> pdb=" O LEU 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 186 Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 217 removed outlier: 3.970A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) Processing helix chain '7' and resid 239 through 248 removed outlier: 3.682A pdb=" N GLN 7 243 " --> pdb=" O ALA 7 239 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET 7 244 " --> pdb=" O ASP 7 240 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP 7 248 " --> pdb=" O MET 7 244 " (cutoff:3.500A) Processing helix chain '7' and resid 322 through 333 Processing helix chain '7' and resid 363 through 374 removed outlier: 3.686A pdb=" N MET 7 373 " --> pdb=" O SER 7 369 " (cutoff:3.500A) Processing helix chain '7' and resid 391 through 404 Processing helix chain '7' and resid 413 through 427 Processing helix chain '7' and resid 431 through 433 No H-bonds generated for 'chain '7' and resid 431 through 433' Processing helix chain '7' and resid 457 through 462 Processing helix chain '7' and resid 467 through 480 removed outlier: 3.588A pdb=" N VAL 7 473 " --> pdb=" O ASP 7 469 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG 7 480 " --> pdb=" O PHE 7 476 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 493 Processing helix chain '7' and resid 499 through 505 removed outlier: 4.017A pdb=" N SER 7 503 " --> pdb=" O ARG 7 499 " (cutoff:3.500A) Processing helix chain '7' and resid 523 through 525 No H-bonds generated for 'chain '7' and resid 523 through 525' Processing helix chain '7' and resid 526 through 531 Processing helix chain '7' and resid 539 through 547 Processing helix chain '7' and resid 562 through 572 removed outlier: 3.799A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 583 removed outlier: 3.660A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR 7 581 " --> pdb=" O ARG 7 577 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET 7 583 " --> pdb=" O LEU 7 579 " (cutoff:3.500A) Processing helix chain '7' and resid 584 through 601 removed outlier: 3.584A pdb=" N ARG 7 601 " --> pdb=" O TYR 7 597 " (cutoff:3.500A) Processing helix chain '7' and resid 611 through 623 Processing helix chain '7' and resid 632 through 646 Processing helix chain '7' and resid 655 through 660 removed outlier: 4.346A pdb=" N THR 7 660 " --> pdb=" O VAL 7 657 " (cutoff:3.500A) Processing helix chain '7' and resid 679 through 689 removed outlier: 3.725A pdb=" N GLU 7 683 " --> pdb=" O SER 7 679 " (cutoff:3.500A) Processing helix chain '7' and resid 693 through 697 removed outlier: 4.512A pdb=" N ASN 7 697 " --> pdb=" O LYS 7 694 " (cutoff:3.500A) Processing helix chain '7' and resid 713 through 723 removed outlier: 4.076A pdb=" N TYR 7 717 " --> pdb=" O THR 7 713 " (cutoff:3.500A) Processing helix chain '7' and resid 723 through 730 Processing helix chain '7' and resid 752 through 765 Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 285 through 304 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1410 through 1415 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.698A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 133 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 156 through 169 removed outlier: 4.062A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'F' and resid 89 through 103 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.726A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'W' and resid 3 through 21 removed outlier: 3.857A pdb=" N ASP W 7 " --> pdb=" O ARG W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 35 removed outlier: 3.916A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 48 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 117 removed outlier: 3.506A pdb=" N SER W 117 " --> pdb=" O LEU W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 137 Processing helix chain 'W' and resid 164 through 192 Proline residue: W 181 - end of helix Processing helix chain 'W' and resid 198 through 203 Processing helix chain 'W' and resid 204 through 206 No H-bonds generated for 'chain 'W' and resid 204 through 206' Processing helix chain 'W' and resid 266 through 288 removed outlier: 3.603A pdb=" N ASN W 288 " --> pdb=" O LYS W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 291 through 295 Processing helix chain 'W' and resid 350 through 369 Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'X' and resid 206 through 212 removed outlier: 3.704A pdb=" N ASP X 212 " --> pdb=" O LYS X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 256 through 266 Processing helix chain 'X' and resid 273 through 282 Processing helix chain 'X' and resid 289 through 293 Processing sheet with id=AA1, first strand: chain '0' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain '0' and resid 174 through 175 removed outlier: 6.792A pdb=" N ARG 0 104 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ILE 0 207 " --> pdb=" O ARG 0 104 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N SER 0 209 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER 0 38 " --> pdb=" O ILE 0 458 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASN 0 37 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN 0 480 " --> pdb=" O ASN 0 37 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE 0 39 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER 0 482 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU 0 41 " --> pdb=" O SER 0 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 250 through 253 Processing sheet with id=AA4, first strand: chain '0' and resid 568 through 571 removed outlier: 6.274A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET 0 537 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY 0 536 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU 0 621 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL 0 620 " --> pdb=" O VAL 0 680 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA 0 682 " --> pdb=" O VAL 0 620 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET 0 622 " --> pdb=" O ALA 0 682 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET 0 495 " --> pdb=" O LEU 0 681 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain '1' and resid 246 through 252 removed outlier: 6.151A pdb=" N VAL 1 247 " --> pdb=" O HIS W 261 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASN W 263 " --> pdb=" O VAL 1 247 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL 1 249 " --> pdb=" O ASN W 263 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR W 265 " --> pdb=" O VAL 1 249 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU 1 251 " --> pdb=" O THR W 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '2' and resid 57 through 58 Processing sheet with id=AA8, first strand: chain '2' and resid 175 through 176 Processing sheet with id=AA9, first strand: chain '2' and resid 237 through 238 removed outlier: 3.582A pdb=" N TYR 2 237 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE 2 269 " --> pdb=" O TYR 2 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '2' and resid 339 through 341 removed outlier: 6.339A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N PHE 7 118 " --> pdb=" O LYS 2 367 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG 2 369 " --> pdb=" O PHE 7 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 481 through 485 removed outlier: 6.531A pdb=" N PHE 2 492 " --> pdb=" O LEU 2 482 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS 2 484 " --> pdb=" O LYS 2 490 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS 2 490 " --> pdb=" O LYS 2 484 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU 5 41 " --> pdb=" O GLU 5 34 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU 5 34 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain '3' and resid 52 through 53 removed outlier: 4.063A pdb=" N ALA 3 52 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU 3 63 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '4' and resid 82 through 87 removed outlier: 6.352A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ASP 4 211 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU 4 176 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 295 through 296 removed outlier: 4.247A pdb=" N MET 6 369 " --> pdb=" O LYS 6 321 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY 6 323 " --> pdb=" O MET 6 369 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 178 through 186 removed outlier: 6.651A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN 6 184 " --> pdb=" O MET 6 169 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET 6 169 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER 6 125 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU 6 233 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE 6 127 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL 6 235 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR 6 129 " --> pdb=" O VAL 6 235 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG 6 230 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LYS 6 262 " --> pdb=" O ARG 6 230 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL 6 232 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU 6 264 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE 6 234 " --> pdb=" O LEU 6 264 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LYS 6 289 " --> pdb=" O VAL 6 261 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL 6 263 " --> pdb=" O LYS 6 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 326 through 328 removed outlier: 3.749A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '6' and resid 334 through 335 Processing sheet with id=AC1, first strand: chain '6' and resid 390 through 391 removed outlier: 3.883A pdb=" N ALA 6 390 " --> pdb=" O ARG 6 428 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG 6 428 " --> pdb=" O ALA 6 390 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 132 through 134 removed outlier: 6.358A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 226 through 227 removed outlier: 4.547A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 340 through 341 Processing sheet with id=AC5, first strand: chain '7' and resid 435 through 438 removed outlier: 4.230A pdb=" N THR 7 456 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE 7 408 " --> pdb=" O ILE 7 486 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP 7 488 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU 7 410 " --> pdb=" O ASP 7 488 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY 7 483 " --> pdb=" O ALA 7 507 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE 7 383 " --> pdb=" O LYS 7 534 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR 7 536 " --> pdb=" O ILE 7 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 651 through 653 removed outlier: 6.481A pdb=" N ILE 7 605 " --> pdb=" O ILE 7 652 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS 7 604 " --> pdb=" O CYS 7 669 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE 7 671 " --> pdb=" O LYS 7 604 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE 7 606 " --> pdb=" O ILE 7 671 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR 7 668 " --> pdb=" O PHE 7 704 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR 7 706 " --> pdb=" O THR 7 668 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU 7 670 " --> pdb=" O TYR 7 706 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU 7 708 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN 7 672 " --> pdb=" O LEU 7 708 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N SER 7 710 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE 7 705 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS 7 734 " --> pdb=" O CYS 7 554 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AC8, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AC9, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.674A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 144 through 147 removed outlier: 5.183A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD3, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AD5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.523A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AD7, first strand: chain 'W' and resid 38 through 39 Processing sheet with id=AD8, first strand: chain 'W' and resid 130 through 131 Processing sheet with id=AD9, first strand: chain 'X' and resid 230 through 234 removed outlier: 4.354A pdb=" N TYR X 243 " --> pdb=" O LEU X 233 " (cutoff:3.500A) 1679 hydrogen bonds defined for protein. 4788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 14227 1.41 - 1.63: 21261 1.63 - 1.85: 317 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 35817 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" F2 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C TYR 0 616 " pdb=" O TYR 0 616 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.20e+01 bond pdb=" F3 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 35812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 48106 2.32 - 4.64: 274 4.64 - 6.96: 17 6.96 - 9.28: 6 9.28 - 11.60: 2 Bond angle restraints: 48405 Sorted by residual: angle pdb=" N PHE 7 565 " pdb=" CA PHE 7 565 " pdb=" C PHE 7 565 " ideal model delta sigma weight residual 111.28 117.10 -5.82 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N ASP 0 613 " pdb=" CA ASP 0 613 " pdb=" C ASP 0 613 " ideal model delta sigma weight residual 110.46 116.89 -6.43 1.48e+00 4.57e-01 1.89e+01 angle pdb=" N3 DT N 67 " pdb=" C4 DT N 67 " pdb=" O4 DT N 67 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT T 39 " pdb=" C4 DT T 39 " pdb=" O4 DT T 39 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT T 36 " pdb=" C4 DT T 36 " pdb=" O4 DT T 36 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 48400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 20742 23.68 - 47.36: 1071 47.36 - 71.03: 117 71.03 - 94.71: 44 94.71 - 118.39: 2 Dihedral angle restraints: 21976 sinusoidal: 9272 harmonic: 12704 Sorted by residual: dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 58.39 -118.39 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -175.26 115.27 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" O1B ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " pdb=" PA ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 1.79 -61.80 1 2.00e+01 2.50e-03 1.27e+01 ... (remaining 21973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 5070 0.076 - 0.153: 428 0.153 - 0.229: 3 0.229 - 0.305: 0 0.305 - 0.381: 2 Chirality restraints: 5503 Sorted by residual: chirality pdb=" CA PHE 7 565 " pdb=" N PHE 7 565 " pdb=" C PHE 7 565 " pdb=" CB PHE 7 565 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PHE 6 301 " pdb=" N PHE 6 301 " pdb=" C PHE 6 301 " pdb=" CB PHE 6 301 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 5500 not shown) Planarity restraints: 6101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP 0 613 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASP 0 613 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP 0 613 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS 0 614 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 7 565 " -0.008 2.00e-02 2.50e+03 1.65e-02 4.76e+00 pdb=" CG PHE 7 565 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE 7 565 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE 7 565 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE 7 565 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE 7 565 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE 7 565 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 13 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO 5 14 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO 5 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 5 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 6098 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 250 2.58 - 3.16: 29573 3.16 - 3.74: 52834 3.74 - 4.32: 72722 4.32 - 4.90: 122627 Nonbonded interactions: 278006 Sorted by model distance: nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.120 nonbonded pdb="MG MG 7 902 " pdb=" O1B ADP 7 903 " model vdw 2.001 2.170 nonbonded pdb=" O PHE 0 529 " pdb=" OG1 THR 0 533 " model vdw 2.025 3.040 nonbonded pdb=" OD1 ASN 5 43 " pdb=" OG SER 5 45 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR 3 35 " pdb=" OD2 ASP 3 83 " model vdw 2.073 3.040 ... (remaining 278001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.530 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.489 35866 Z= 0.296 Angle : 0.475 11.600 48474 Z= 0.276 Chirality : 0.039 0.381 5503 Planarity : 0.002 0.047 6101 Dihedral : 14.103 118.391 13696 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 2.39 (0.14), residues: 4226 helix: 3.11 (0.12), residues: 1947 sheet: 0.42 (0.24), residues: 513 loop : 0.23 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 519 TYR 0.015 0.001 TYR 7 581 PHE 0.034 0.001 PHE 7 565 TRP 0.007 0.001 TRP 2 201 HIS 0.002 0.000 HIS W 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (35817) covalent geometry : angle 0.45893 / 0.28 (48405) hydrogen bonds : bond 0.20519 / 13.55 ( 1679) hydrogen bonds : angle 6.08053 / 4.36 ( 4788) metal coordination : bond 0.00477 / 0.23 ( 48) metal coordination : angle 3.27157 / 1.82 ( 69) Misc. bond : bond 0.48869 / 25.72 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 901 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7620 (mttt) cc_final: 0.6996 (mmtp) REVERT: 0 80 GLU cc_start: 0.7291 (tp30) cc_final: 0.6954 (mm-30) REVERT: 0 131 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6162 (mm-30) REVERT: 0 183 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7326 (mtmm) REVERT: 0 197 ARG cc_start: 0.6935 (mtp180) cc_final: 0.6597 (ttm-80) REVERT: 0 253 THR cc_start: 0.7986 (p) cc_final: 0.7750 (m) REVERT: 0 259 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7331 (mtm110) REVERT: 0 365 GLN cc_start: 0.7676 (tt0) cc_final: 0.7346 (tt0) REVERT: 0 397 THR cc_start: 0.8335 (t) cc_final: 0.8116 (m) REVERT: 0 434 ILE cc_start: 0.8629 (tt) cc_final: 0.8380 (tt) REVERT: 0 452 ARG cc_start: 0.8325 (ttt90) cc_final: 0.8033 (ttt180) REVERT: 0 476 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7943 (mtpt) REVERT: 0 528 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6830 (mm-30) REVERT: 0 544 TYR cc_start: 0.8542 (t80) cc_final: 0.8255 (t80) REVERT: 0 659 MET cc_start: 0.9001 (mmm) cc_final: 0.8672 (mmp) REVERT: 0 684 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7473 (ttp80) REVERT: 1 29 TRP cc_start: 0.8555 (t60) cc_final: 0.8353 (t60) REVERT: 1 33 ASP cc_start: 0.7149 (t0) cc_final: 0.6897 (t0) REVERT: 1 192 MET cc_start: 0.6388 (ttt) cc_final: 0.6119 (ttm) REVERT: 1 331 HIS cc_start: 0.7494 (p90) cc_final: 0.7279 (p90) REVERT: 1 338 ASP cc_start: 0.8218 (t0) cc_final: 0.6937 (t0) REVERT: 1 417 ASN cc_start: 0.7792 (m110) cc_final: 0.7541 (m-40) REVERT: 1 501 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8228 (tttp) REVERT: 1 504 ILE cc_start: 0.9072 (mm) cc_final: 0.8690 (mt) REVERT: 1 507 ILE cc_start: 0.9056 (mt) cc_final: 0.8724 (mt) REVERT: 1 552 MET cc_start: 0.7620 (ttm) cc_final: 0.7394 (mtp) REVERT: 1 561 LEU cc_start: 0.9112 (tp) cc_final: 0.8844 (tp) REVERT: 1 628 HIS cc_start: 0.7715 (t-90) cc_final: 0.7331 (t-170) REVERT: 2 48 MET cc_start: 0.8339 (tpp) cc_final: 0.7973 (tpp) REVERT: 2 201 TRP cc_start: 0.8040 (m100) cc_final: 0.7735 (m100) REVERT: 2 247 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7928 (mmt90) REVERT: 2 249 MET cc_start: 0.8348 (tmm) cc_final: 0.8142 (tmm) REVERT: 2 277 MET cc_start: 0.7033 (tpp) cc_final: 0.6702 (tpp) REVERT: 3 46 ILE cc_start: 0.8903 (mt) cc_final: 0.8503 (mm) REVERT: 4 321 LYS cc_start: 0.8255 (mttt) cc_final: 0.7793 (mtpp) REVERT: 6 139 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7594 (mmtm) REVERT: 6 180 GLN cc_start: 0.7628 (tt0) cc_final: 0.7218 (tt0) REVERT: 6 252 ASP cc_start: 0.7332 (t0) cc_final: 0.6775 (m-30) REVERT: 6 348 PHE cc_start: 0.7885 (m-10) cc_final: 0.7546 (m-10) REVERT: 6 433 LYS cc_start: 0.8455 (mttt) cc_final: 0.7958 (mmtt) REVERT: 6 441 ASP cc_start: 0.7321 (t0) cc_final: 0.6745 (t0) REVERT: 7 214 LYS cc_start: 0.8299 (mtpp) cc_final: 0.8013 (mtpp) REVERT: 7 341 TYR cc_start: 0.8287 (t80) cc_final: 0.7764 (t80) REVERT: 7 370 LEU cc_start: 0.8617 (tp) cc_final: 0.8346 (tt) REVERT: 7 526 ASP cc_start: 0.7492 (m-30) cc_final: 0.7239 (m-30) REVERT: 7 603 ASP cc_start: 0.7071 (m-30) cc_final: 0.6842 (m-30) REVERT: 7 645 TYR cc_start: 0.7371 (m-80) cc_final: 0.6828 (m-10) REVERT: 7 666 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7445 (mm-30) REVERT: 7 722 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7940 (ttt-90) REVERT: 7 750 TYR cc_start: 0.8981 (m-80) cc_final: 0.8756 (m-80) REVERT: A 146 MET cc_start: 0.7439 (mmm) cc_final: 0.7183 (mmm) REVERT: A 169 ASN cc_start: 0.8317 (m-40) cc_final: 0.7630 (m110) REVERT: A 226 GLU cc_start: 0.6845 (tt0) cc_final: 0.6568 (tt0) REVERT: A 493 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7055 (mm-40) REVERT: A 495 GLU cc_start: 0.7694 (tp30) cc_final: 0.7240 (mm-30) REVERT: A 1398 MET cc_start: 0.5957 (ttt) cc_final: 0.5695 (ttm) REVERT: A 1428 VAL cc_start: 0.7243 (t) cc_final: 0.7024 (t) REVERT: B 1210 MET cc_start: 0.5830 (mtt) cc_final: 0.5520 (mtt) REVERT: B 1212 ILE cc_start: 0.7089 (mm) cc_final: 0.6785 (mt) REVERT: D 36 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7644 (mtpp) REVERT: D 38 ILE cc_start: 0.8641 (mt) cc_final: 0.8256 (tp) REVERT: F 104 ASN cc_start: 0.8338 (t0) cc_final: 0.7932 (t0) REVERT: G 23 LYS cc_start: 0.8103 (mttm) cc_final: 0.7617 (mttt) REVERT: G 29 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7395 (tptm) REVERT: G 160 ILE cc_start: 0.8432 (pt) cc_final: 0.8179 (mt) REVERT: W 45 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7761 (tm-30) REVERT: W 108 ARG cc_start: 0.7742 (ttm170) cc_final: 0.7526 (ttm170) REVERT: W 123 MET cc_start: 0.6370 (ttp) cc_final: 0.6126 (ttt) REVERT: W 178 GLN cc_start: 0.7972 (mt0) cc_final: 0.7625 (mt0) REVERT: X 208 LYS cc_start: 0.8780 (tptp) cc_final: 0.8568 (tptt) REVERT: X 261 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7872 (ttpp) outliers start: 0 outliers final: 0 residues processed: 901 average time/residue: 0.2395 time to fit residues: 346.5988 Evaluate side-chains 671 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 671 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 60 GLN 0 239 ASN 0 291 GLN 0 707 ASN 1 87 HIS 1 262 ASN 1 510 ASN 1 585 HIS 2 12 GLN 2 22 GLN 2 261 GLN 2 395 GLN 4 226 GLN 5 64 ASN 6 445 HIS 6 450 ASN 7 729 GLN D 31 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.190525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132835 restraints weight = 43460.336| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.61 r_work: 0.2968 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35866 Z= 0.200 Angle : 0.629 13.127 48474 Z= 0.319 Chirality : 0.043 0.198 5503 Planarity : 0.004 0.047 6101 Dihedral : 7.855 120.529 4888 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.74 % Allowed : 8.57 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.72 (0.13), residues: 4226 helix: 2.31 (0.12), residues: 2003 sheet: 0.28 (0.24), residues: 484 loop : 0.06 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG 7 378 TYR 0.019 0.002 TYR 4 130 PHE 0.022 0.002 PHE 1 9 TRP 0.012 0.002 TRP 2 201 HIS 0.006 0.001 HIS W 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (35817) covalent geometry : angle 0.61041 / 0.32 (48405) hydrogen bonds : bond 0.05477 / 3.66 ( 1679) hydrogen bonds : angle 4.74821 / 3.37 ( 4788) metal coordination : bond 0.01176 / 0.69 ( 48) metal coordination : angle 4.12244 / 2.52 ( 69) Misc. bond : bond 0.00795 / 0.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 704 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7832 (mttt) cc_final: 0.7195 (mmtp) REVERT: 0 78 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7117 (mm-30) REVERT: 0 131 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6168 (mm-30) REVERT: 0 183 LYS cc_start: 0.7612 (ttmt) cc_final: 0.6922 (mtmm) REVERT: 0 190 LEU cc_start: 0.8452 (mt) cc_final: 0.8248 (mt) REVERT: 0 197 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6920 (ttm-80) REVERT: 0 259 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7536 (mtm110) REVERT: 0 365 GLN cc_start: 0.8187 (tt0) cc_final: 0.7817 (tt0) REVERT: 0 397 THR cc_start: 0.8544 (t) cc_final: 0.8277 (m) REVERT: 0 413 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: 0 423 TYR cc_start: 0.8065 (m-80) cc_final: 0.7797 (m-10) REVERT: 0 452 ARG cc_start: 0.8504 (ttt90) cc_final: 0.8183 (ttt180) REVERT: 0 476 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8385 (mtpt) REVERT: 0 528 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7469 (mm-30) REVERT: 0 544 TYR cc_start: 0.8753 (t80) cc_final: 0.8485 (t80) REVERT: 0 620 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (p) REVERT: 0 684 ARG cc_start: 0.8568 (ttp-170) cc_final: 0.8325 (ttp80) REVERT: 1 11 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8660 (mmmt) REVERT: 1 57 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7160 (pttp) REVERT: 1 192 MET cc_start: 0.6960 (ttt) cc_final: 0.6374 (ttt) REVERT: 1 295 LYS cc_start: 0.8909 (tttp) cc_final: 0.8654 (tttp) REVERT: 1 302 MET cc_start: 0.7247 (tmm) cc_final: 0.6767 (tmm) REVERT: 1 363 ASP cc_start: 0.8189 (t0) cc_final: 0.7827 (t0) REVERT: 1 365 ASN cc_start: 0.8164 (m110) cc_final: 0.7654 (m-40) REVERT: 1 417 ASN cc_start: 0.7927 (m110) cc_final: 0.7566 (m-40) REVERT: 1 427 SER cc_start: 0.7819 (m) cc_final: 0.7608 (t) REVERT: 1 501 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8246 (tttp) REVERT: 1 507 ILE cc_start: 0.9068 (mt) cc_final: 0.8702 (mt) REVERT: 1 548 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7408 (tm-30) REVERT: 1 552 MET cc_start: 0.7945 (ttm) cc_final: 0.7618 (mtp) REVERT: 1 561 LEU cc_start: 0.8646 (tp) cc_final: 0.8330 (tp) REVERT: 1 581 LYS cc_start: 0.8091 (mttm) cc_final: 0.7461 (ttpt) REVERT: 2 22 GLN cc_start: 0.7673 (mt0) cc_final: 0.7410 (mt0) REVERT: 2 48 MET cc_start: 0.7930 (tpp) cc_final: 0.7012 (tpp) REVERT: 2 184 ILE cc_start: 0.8522 (mp) cc_final: 0.8230 (mt) REVERT: 2 216 MET cc_start: 0.7882 (pmm) cc_final: 0.7319 (pmm) REVERT: 2 247 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.8180 (mtp85) REVERT: 2 249 MET cc_start: 0.8411 (tmm) cc_final: 0.8131 (tmm) REVERT: 2 255 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7637 (t0) REVERT: 2 373 MET cc_start: 0.8385 (ppp) cc_final: 0.8056 (ptt) REVERT: 3 37 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8035 (ttp80) REVERT: 3 46 ILE cc_start: 0.8647 (mt) cc_final: 0.8314 (mm) REVERT: 3 53 GLN cc_start: 0.8592 (tt0) cc_final: 0.8360 (tt0) REVERT: 4 303 ASN cc_start: 0.7742 (t0) cc_final: 0.7481 (t0) REVERT: 4 321 LYS cc_start: 0.7938 (mttt) cc_final: 0.7580 (mtpp) REVERT: 6 139 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7851 (mmtm) REVERT: 6 158 HIS cc_start: 0.7733 (m-70) cc_final: 0.7476 (m-70) REVERT: 6 168 GLN cc_start: 0.8290 (pm20) cc_final: 0.7868 (pm20) REVERT: 6 252 ASP cc_start: 0.7622 (t0) cc_final: 0.6907 (m-30) REVERT: 6 299 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7547 (mm-30) REVERT: 6 348 PHE cc_start: 0.7618 (m-10) cc_final: 0.7335 (m-80) REVERT: 6 433 LYS cc_start: 0.8547 (mttt) cc_final: 0.7814 (mmtt) REVERT: 7 124 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7299 (mtt90) REVERT: 7 138 ASP cc_start: 0.7581 (t0) cc_final: 0.7338 (t0) REVERT: 7 214 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8070 (mtpp) REVERT: 7 244 MET cc_start: 0.6907 (tmm) cc_final: 0.5461 (mtm) REVERT: 7 341 TYR cc_start: 0.8205 (t80) cc_final: 0.7855 (t80) REVERT: 7 355 ASP cc_start: 0.7634 (m-30) cc_final: 0.7387 (m-30) REVERT: 7 362 ILE cc_start: 0.8218 (mm) cc_final: 0.7807 (mt) REVERT: 7 367 GLU cc_start: 0.7213 (tp30) cc_final: 0.6603 (tp30) REVERT: 7 459 MET cc_start: 0.8028 (mmm) cc_final: 0.7785 (mmm) REVERT: 7 564 GLU cc_start: 0.8430 (tp30) cc_final: 0.7996 (tp30) REVERT: 7 568 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: 7 578 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7291 (mtt) REVERT: 7 603 ASP cc_start: 0.7853 (m-30) cc_final: 0.7638 (m-30) REVERT: 7 645 TYR cc_start: 0.7434 (m-80) cc_final: 0.6961 (m-10) REVERT: 7 666 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8083 (mm-30) REVERT: 7 729 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7813 (mm110) REVERT: A 146 MET cc_start: 0.7660 (mmm) cc_final: 0.7317 (mmm) REVERT: A 169 ASN cc_start: 0.8434 (m-40) cc_final: 0.7605 (m110) REVERT: A 226 GLU cc_start: 0.7513 (tt0) cc_final: 0.7179 (tt0) REVERT: A 1398 MET cc_start: 0.6326 (ttt) cc_final: 0.5922 (ttm) REVERT: A 1428 VAL cc_start: 0.8136 (t) cc_final: 0.7923 (t) REVERT: A 1446 ASP cc_start: 0.7610 (t0) cc_final: 0.7057 (p0) REVERT: B 1151 LEU cc_start: 0.6553 (mt) cc_final: 0.6352 (mt) REVERT: B 1210 MET cc_start: 0.6724 (mtt) cc_final: 0.6472 (mtt) REVERT: D 31 GLN cc_start: 0.7884 (tp40) cc_final: 0.7643 (tp40) REVERT: D 36 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7812 (mtpp) REVERT: F 104 ASN cc_start: 0.8832 (t0) cc_final: 0.8431 (t0) REVERT: F 122 MET cc_start: 0.4117 (mtt) cc_final: 0.3909 (mtt) REVERT: G 96 GLN cc_start: 0.7583 (pm20) cc_final: 0.7309 (pm20) REVERT: W 45 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7890 (tm-30) REVERT: W 108 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7527 (ttm170) REVERT: W 115 LYS cc_start: 0.8917 (tptp) cc_final: 0.8523 (tptp) REVERT: W 123 MET cc_start: 0.6595 (ttp) cc_final: 0.6101 (ttt) REVERT: W 174 ARG cc_start: 0.8441 (mtm180) cc_final: 0.7851 (ttp-110) REVERT: W 178 GLN cc_start: 0.8315 (mt0) cc_final: 0.7836 (mt0) REVERT: W 212 GLN cc_start: 0.8828 (mt0) cc_final: 0.8617 (mp10) REVERT: X 208 LYS cc_start: 0.8824 (tptp) cc_final: 0.8474 (tptt) REVERT: X 261 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7885 (ttpp) REVERT: X 262 MET cc_start: 0.8381 (mtt) cc_final: 0.8108 (mtm) outliers start: 68 outliers final: 35 residues processed: 738 average time/residue: 0.2316 time to fit residues: 275.6562 Evaluate side-chains 711 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 670 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 401 ASP Chi-restraints excluded: chain 0 residue 413 GLU Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 278 PHE Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 218 LEU Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 255 ASP Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 49 SER Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 295 THR Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 6 residue 450 ASN Chi-restraints excluded: chain 7 residue 116 HIS Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 7 residue 568 GLU Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 417 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 361 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 347 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 87 HIS 1 510 ASN 1 513 GLN 1 628 HIS 4 62 ASN 4 226 GLN 5 64 ASN 7 761 GLN A 213 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.189017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130295 restraints weight = 43434.595| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.63 r_work: 0.2987 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 35866 Z= 0.145 Angle : 0.556 11.922 48474 Z= 0.281 Chirality : 0.040 0.163 5503 Planarity : 0.004 0.048 6101 Dihedral : 7.891 116.957 4888 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.51 % Allowed : 11.31 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.63 (0.13), residues: 4226 helix: 2.26 (0.12), residues: 2002 sheet: 0.11 (0.24), residues: 495 loop : 0.04 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 281 TYR 0.026 0.001 TYR 7 750 PHE 0.017 0.001 PHE 0 334 TRP 0.010 0.001 TRP 7 427 HIS 0.004 0.001 HIS W 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (35817) covalent geometry : angle 0.53685 / 0.28 (48405) hydrogen bonds : bond 0.04519 / 3.01 ( 1679) hydrogen bonds : angle 4.44458 / 3.16 ( 4788) metal coordination : bond 0.00697 / 0.38 ( 48) metal coordination : angle 3.85439 / 2.29 ( 69) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 682 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7849 (mttt) cc_final: 0.7155 (mmtp) REVERT: 0 131 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6313 (mm-30) REVERT: 0 183 LYS cc_start: 0.7649 (ttmt) cc_final: 0.6944 (mtmm) REVERT: 0 197 ARG cc_start: 0.7293 (mtp180) cc_final: 0.6913 (ttm-80) REVERT: 0 255 ASP cc_start: 0.7704 (t0) cc_final: 0.7066 (t0) REVERT: 0 259 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7507 (mtt-85) REVERT: 0 386 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7970 (tmm-80) REVERT: 0 397 THR cc_start: 0.8534 (t) cc_final: 0.8251 (m) REVERT: 0 452 ARG cc_start: 0.8508 (ttt90) cc_final: 0.8205 (ttt180) REVERT: 0 476 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8405 (mtpt) REVERT: 0 528 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7479 (mm-30) REVERT: 0 584 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7347 (tt0) REVERT: 0 620 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (p) REVERT: 0 684 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.7954 (ptm-80) REVERT: 1 11 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8599 (mmmt) REVERT: 1 45 ILE cc_start: 0.9191 (mm) cc_final: 0.8963 (mm) REVERT: 1 57 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7419 (pttp) REVERT: 1 252 SER cc_start: 0.8203 (m) cc_final: 0.7999 (t) REVERT: 1 295 LYS cc_start: 0.8952 (tttp) cc_final: 0.8721 (tttp) REVERT: 1 302 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6513 (tmm) REVERT: 1 326 ASP cc_start: 0.7040 (m-30) cc_final: 0.6666 (t70) REVERT: 1 338 ASP cc_start: 0.8295 (t0) cc_final: 0.7528 (t0) REVERT: 1 363 ASP cc_start: 0.8182 (t0) cc_final: 0.7857 (t0) REVERT: 1 501 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8179 (tttp) REVERT: 1 507 ILE cc_start: 0.9104 (mt) cc_final: 0.8724 (mt) REVERT: 1 548 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7389 (tm-30) REVERT: 1 552 MET cc_start: 0.7930 (ttm) cc_final: 0.7553 (mtp) REVERT: 1 561 LEU cc_start: 0.8684 (tp) cc_final: 0.8365 (tp) REVERT: 1 581 LYS cc_start: 0.8087 (mttm) cc_final: 0.7463 (ttpt) REVERT: 2 184 ILE cc_start: 0.8533 (mp) cc_final: 0.8248 (mt) REVERT: 2 210 MET cc_start: 0.8078 (mtp) cc_final: 0.7719 (mtp) REVERT: 2 216 MET cc_start: 0.7819 (pmm) cc_final: 0.7425 (pmm) REVERT: 2 247 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.8150 (mtp85) REVERT: 2 249 MET cc_start: 0.8457 (tmm) cc_final: 0.8224 (tmm) REVERT: 2 253 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6692 (mmm) REVERT: 2 255 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7497 (t0) REVERT: 2 373 MET cc_start: 0.8386 (ppp) cc_final: 0.8068 (ptt) REVERT: 2 410 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7843 (tmm-80) REVERT: 3 11 ASP cc_start: 0.8540 (t0) cc_final: 0.8004 (t0) REVERT: 3 19 ASP cc_start: 0.7587 (t70) cc_final: 0.7086 (t0) REVERT: 3 21 TYR cc_start: 0.8230 (t80) cc_final: 0.7901 (t80) REVERT: 3 37 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8104 (ttp80) REVERT: 3 38 ILE cc_start: 0.8298 (tt) cc_final: 0.7856 (pt) REVERT: 3 40 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7920 (tm-30) REVERT: 3 46 ILE cc_start: 0.8701 (mt) cc_final: 0.8363 (mm) REVERT: 3 53 GLN cc_start: 0.8608 (tt0) cc_final: 0.8394 (tt0) REVERT: 3 79 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7897 (tm-30) REVERT: 3 98 ASP cc_start: 0.8895 (t0) cc_final: 0.8584 (t0) REVERT: 3 115 ASP cc_start: 0.8255 (t0) cc_final: 0.7876 (t0) REVERT: 3 130 GLU cc_start: 0.8087 (tp30) cc_final: 0.7388 (tm-30) REVERT: 4 108 LYS cc_start: 0.8411 (mmpt) cc_final: 0.8157 (mmpt) REVERT: 4 219 LYS cc_start: 0.8679 (tttt) cc_final: 0.8301 (tttp) REVERT: 4 281 ARG cc_start: 0.8364 (ptp90) cc_final: 0.8110 (ptp90) REVERT: 4 321 LYS cc_start: 0.7990 (mttt) cc_final: 0.7579 (mtpp) REVERT: 5 27 MET cc_start: 0.6853 (tmm) cc_final: 0.6463 (tmm) REVERT: 6 139 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7767 (mmtm) REVERT: 6 155 ASP cc_start: 0.7777 (m-30) cc_final: 0.7523 (m-30) REVERT: 6 246 ASP cc_start: 0.8349 (p0) cc_final: 0.7975 (p0) REVERT: 6 252 ASP cc_start: 0.7611 (t0) cc_final: 0.6874 (m-30) REVERT: 6 255 VAL cc_start: 0.8763 (t) cc_final: 0.8534 (t) REVERT: 6 299 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7643 (mm-30) REVERT: 6 327 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7901 (mtp85) REVERT: 6 348 PHE cc_start: 0.7782 (m-10) cc_final: 0.7512 (m-80) REVERT: 6 428 ARG cc_start: 0.8345 (ptp90) cc_final: 0.7888 (ptp90) REVERT: 6 433 LYS cc_start: 0.8554 (mttt) cc_final: 0.7808 (mmtt) REVERT: 7 124 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7381 (mtt90) REVERT: 7 138 ASP cc_start: 0.7569 (t0) cc_final: 0.7297 (t0) REVERT: 7 214 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8218 (mtpp) REVERT: 7 244 MET cc_start: 0.6948 (tmm) cc_final: 0.5425 (mtm) REVERT: 7 341 TYR cc_start: 0.8284 (t80) cc_final: 0.7889 (t80) REVERT: 7 355 ASP cc_start: 0.7650 (m-30) cc_final: 0.7435 (m-30) REVERT: 7 362 ILE cc_start: 0.8196 (mm) cc_final: 0.7759 (mt) REVERT: 7 367 GLU cc_start: 0.7236 (tp30) cc_final: 0.6517 (tp30) REVERT: 7 564 GLU cc_start: 0.8491 (tp30) cc_final: 0.8111 (tp30) REVERT: 7 568 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: 7 578 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7412 (mtt) REVERT: 7 603 ASP cc_start: 0.7857 (m-30) cc_final: 0.7641 (m-30) REVERT: 7 617 GLU cc_start: 0.7857 (tt0) cc_final: 0.7597 (mt-10) REVERT: 7 645 TYR cc_start: 0.7419 (m-80) cc_final: 0.6898 (m-10) REVERT: 7 666 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 146 MET cc_start: 0.7734 (mmm) cc_final: 0.7392 (mmm) REVERT: A 169 ASN cc_start: 0.8481 (m-40) cc_final: 0.7662 (m110) REVERT: A 226 GLU cc_start: 0.7586 (tt0) cc_final: 0.7244 (tt0) REVERT: A 1398 MET cc_start: 0.6347 (ttt) cc_final: 0.5940 (ttm) REVERT: A 1428 VAL cc_start: 0.8176 (t) cc_final: 0.7963 (t) REVERT: A 1446 ASP cc_start: 0.7664 (t0) cc_final: 0.7092 (p0) REVERT: B 1210 MET cc_start: 0.6694 (mtt) cc_final: 0.6430 (mtt) REVERT: D 31 GLN cc_start: 0.7825 (tp40) cc_final: 0.7503 (tp40) REVERT: D 36 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7852 (mtpp) REVERT: F 104 ASN cc_start: 0.8910 (t0) cc_final: 0.8473 (t0) REVERT: F 122 MET cc_start: 0.4120 (mtt) cc_final: 0.3911 (mtt) REVERT: G 96 GLN cc_start: 0.7648 (pm20) cc_final: 0.7374 (pm20) REVERT: G 115 MET cc_start: 0.8473 (mtp) cc_final: 0.8252 (mtm) REVERT: W 45 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7978 (tm-30) REVERT: W 108 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7715 (ttm170) REVERT: W 115 LYS cc_start: 0.8916 (tptp) cc_final: 0.8581 (tptp) REVERT: W 123 MET cc_start: 0.6552 (ttp) cc_final: 0.6119 (ttt) REVERT: W 174 ARG cc_start: 0.8390 (mtm180) cc_final: 0.7810 (ttp-110) REVERT: W 178 GLN cc_start: 0.8260 (mt0) cc_final: 0.7781 (mt0) REVERT: W 212 GLN cc_start: 0.8781 (mt0) cc_final: 0.8467 (mp10) REVERT: X 208 LYS cc_start: 0.8847 (tptp) cc_final: 0.8467 (tptt) REVERT: X 261 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7887 (ttpp) REVERT: X 262 MET cc_start: 0.8353 (mtt) cc_final: 0.8021 (mtm) REVERT: X 317 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5581 (ttp) outliers start: 59 outliers final: 37 residues processed: 707 average time/residue: 0.2280 time to fit residues: 260.3770 Evaluate side-chains 687 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 642 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 278 PHE Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 218 LEU Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 255 ASP Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 224 VAL Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 415 VAL Chi-restraints excluded: chain 7 residue 568 GLU Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain X residue 248 SER Chi-restraints excluded: chain X residue 317 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 238 optimal weight: 1.9990 chunk 352 optimal weight: 0.6980 chunk 274 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 39 optimal weight: 0.0060 chunk 370 optimal weight: 0.9980 chunk 256 optimal weight: 0.0060 chunk 290 optimal weight: 0.0570 chunk 76 optimal weight: 0.4980 chunk 147 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 60 GLN 0 291 GLN 2 12 GLN 4 226 GLN 7 642 ASN 7 644 GLN 7 646 ASN G 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.191356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133182 restraints weight = 43031.342| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.59 r_work: 0.3150 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35866 Z= 0.110 Angle : 0.520 14.063 48474 Z= 0.263 Chirality : 0.040 0.160 5503 Planarity : 0.004 0.057 6101 Dihedral : 7.900 117.329 4888 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.89 % Allowed : 12.72 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.61 (0.13), residues: 4226 helix: 2.26 (0.12), residues: 1998 sheet: 0.07 (0.23), residues: 493 loop : 0.02 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 0 668 TYR 0.020 0.001 TYR 7 750 PHE 0.035 0.001 PHE 2 269 TRP 0.012 0.001 TRP X 214 HIS 0.009 0.001 HIS 7 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (35817) covalent geometry : angle 0.50264 / 0.26 (48405) hydrogen bonds : bond 0.03747 / 2.49 ( 1679) hydrogen bonds : angle 4.21135 / 3.00 ( 4788) metal coordination : bond 0.00604 / 0.38 ( 48) metal coordination : angle 3.60415 / 2.04 ( 69) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 672 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7930 (mttt) cc_final: 0.7104 (mmtp) REVERT: 0 78 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7099 (mm-30) REVERT: 0 87 GLU cc_start: 0.7792 (tt0) cc_final: 0.7569 (tt0) REVERT: 0 131 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6278 (mm-30) REVERT: 0 183 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7103 (mtmm) REVERT: 0 259 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7584 (mtm110) REVERT: 0 397 THR cc_start: 0.8466 (t) cc_final: 0.8167 (m) REVERT: 0 452 ARG cc_start: 0.8497 (ttt90) cc_final: 0.8189 (ttt180) REVERT: 0 528 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7445 (mm-30) REVERT: 0 584 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7398 (tt0) REVERT: 0 643 ARG cc_start: 0.7816 (tmm-80) cc_final: 0.7530 (ttp80) REVERT: 0 684 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8035 (ptm-80) REVERT: 1 11 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8562 (mmmt) REVERT: 1 45 ILE cc_start: 0.9205 (mm) cc_final: 0.8991 (mm) REVERT: 1 57 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7453 (pttp) REVERT: 1 252 SER cc_start: 0.8320 (m) cc_final: 0.8118 (t) REVERT: 1 302 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6361 (tmm) REVERT: 1 326 ASP cc_start: 0.7069 (m-30) cc_final: 0.6712 (t70) REVERT: 1 338 ASP cc_start: 0.8350 (t0) cc_final: 0.7539 (t0) REVERT: 1 363 ASP cc_start: 0.8216 (t0) cc_final: 0.7865 (t0) REVERT: 1 365 ASN cc_start: 0.8182 (m110) cc_final: 0.7655 (m-40) REVERT: 1 501 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8120 (tttp) REVERT: 1 507 ILE cc_start: 0.9121 (mt) cc_final: 0.8778 (mt) REVERT: 1 548 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7342 (tm-30) REVERT: 1 552 MET cc_start: 0.7899 (ttm) cc_final: 0.7501 (mtp) REVERT: 1 561 LEU cc_start: 0.8823 (tp) cc_final: 0.8502 (tp) REVERT: 1 581 LYS cc_start: 0.8188 (mttm) cc_final: 0.7582 (ttpt) REVERT: 2 184 ILE cc_start: 0.8447 (mp) cc_final: 0.8153 (mt) REVERT: 2 210 MET cc_start: 0.8122 (mtp) cc_final: 0.7749 (mtp) REVERT: 2 247 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.8141 (mtp85) REVERT: 2 253 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6893 (mmm) REVERT: 2 254 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7404 (ttt90) REVERT: 2 255 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7514 (t0) REVERT: 2 373 MET cc_start: 0.8306 (ppp) cc_final: 0.8002 (ptt) REVERT: 2 410 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7825 (tmm-80) REVERT: 3 11 ASP cc_start: 0.8602 (t0) cc_final: 0.8087 (t0) REVERT: 3 21 TYR cc_start: 0.8221 (t80) cc_final: 0.7985 (t80) REVERT: 3 37 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.8156 (ttp80) REVERT: 3 38 ILE cc_start: 0.8413 (tt) cc_final: 0.7972 (pt) REVERT: 3 40 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7941 (tm-30) REVERT: 3 46 ILE cc_start: 0.8784 (mt) cc_final: 0.8464 (mm) REVERT: 3 79 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7888 (tp30) REVERT: 3 98 ASP cc_start: 0.8826 (t0) cc_final: 0.8481 (t0) REVERT: 3 115 ASP cc_start: 0.8181 (t0) cc_final: 0.7797 (t0) REVERT: 4 281 ARG cc_start: 0.8323 (ptp90) cc_final: 0.7918 (ptp90) REVERT: 4 303 ASN cc_start: 0.8001 (t0) cc_final: 0.7725 (t0) REVERT: 4 321 LYS cc_start: 0.7976 (mttt) cc_final: 0.7611 (mtpp) REVERT: 6 155 ASP cc_start: 0.7833 (m-30) cc_final: 0.7568 (m-30) REVERT: 6 246 ASP cc_start: 0.8344 (p0) cc_final: 0.8050 (p0) REVERT: 6 252 ASP cc_start: 0.7657 (t0) cc_final: 0.6936 (m-30) REVERT: 6 255 VAL cc_start: 0.8733 (t) cc_final: 0.8452 (t) REVERT: 6 303 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7515 (tp30) REVERT: 6 327 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7747 (mtp85) REVERT: 6 348 PHE cc_start: 0.7852 (m-10) cc_final: 0.7599 (m-80) REVERT: 6 357 CYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7273 (m) REVERT: 6 369 MET cc_start: 0.7654 (ttp) cc_final: 0.7441 (ttp) REVERT: 6 433 LYS cc_start: 0.8527 (mttt) cc_final: 0.7836 (mmtt) REVERT: 6 446 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6903 (mt-10) REVERT: 7 118 PHE cc_start: 0.8940 (m-80) cc_final: 0.8687 (m-80) REVERT: 7 121 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8507 (pp) REVERT: 7 124 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7508 (mtt90) REVERT: 7 138 ASP cc_start: 0.7555 (t0) cc_final: 0.7166 (t0) REVERT: 7 211 ASN cc_start: 0.7593 (m-40) cc_final: 0.7350 (m-40) REVERT: 7 214 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8119 (mtpp) REVERT: 7 244 MET cc_start: 0.6865 (tmm) cc_final: 0.5483 (mtm) REVERT: 7 341 TYR cc_start: 0.8265 (t80) cc_final: 0.7889 (t80) REVERT: 7 355 ASP cc_start: 0.7579 (m-30) cc_final: 0.7360 (m-30) REVERT: 7 362 ILE cc_start: 0.8226 (mm) cc_final: 0.7802 (mt) REVERT: 7 367 GLU cc_start: 0.7406 (tp30) cc_final: 0.6694 (tp30) REVERT: 7 568 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: 7 578 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7323 (mtp) REVERT: 7 603 ASP cc_start: 0.7798 (m-30) cc_final: 0.7595 (m-30) REVERT: 7 617 GLU cc_start: 0.7810 (tt0) cc_final: 0.7499 (mt-10) REVERT: 7 645 TYR cc_start: 0.7440 (m-80) cc_final: 0.6915 (m-10) REVERT: 7 651 THR cc_start: 0.8557 (p) cc_final: 0.7989 (t) REVERT: 7 666 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8152 (mm-30) REVERT: 7 764 LEU cc_start: 0.7909 (mt) cc_final: 0.6963 (mt) REVERT: A 146 MET cc_start: 0.7748 (mmm) cc_final: 0.7413 (mmm) REVERT: A 169 ASN cc_start: 0.8538 (m-40) cc_final: 0.7760 (m110) REVERT: A 226 GLU cc_start: 0.7592 (tt0) cc_final: 0.7293 (tt0) REVERT: A 1398 MET cc_start: 0.6386 (ttt) cc_final: 0.6034 (ttm) REVERT: A 1428 VAL cc_start: 0.8302 (t) cc_final: 0.8099 (t) REVERT: A 1446 ASP cc_start: 0.7679 (t0) cc_final: 0.7159 (p0) REVERT: B 1151 LEU cc_start: 0.6809 (mt) cc_final: 0.6607 (mt) REVERT: B 1210 MET cc_start: 0.6754 (mtt) cc_final: 0.6527 (mtt) REVERT: D 31 GLN cc_start: 0.7774 (tp40) cc_final: 0.7433 (tp40) REVERT: D 36 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7980 (mtpp) REVERT: F 104 ASN cc_start: 0.8877 (t0) cc_final: 0.8440 (t0) REVERT: F 122 MET cc_start: 0.4195 (mtt) cc_final: 0.3969 (mtt) REVERT: G 96 GLN cc_start: 0.7751 (pm20) cc_final: 0.7488 (pm20) REVERT: G 114 LEU cc_start: 0.8510 (mm) cc_final: 0.8182 (mt) REVERT: G 115 MET cc_start: 0.8372 (mtp) cc_final: 0.8169 (mtm) REVERT: W 104 GLN cc_start: 0.8628 (tp40) cc_final: 0.8271 (tp40) REVERT: W 123 MET cc_start: 0.6570 (ttp) cc_final: 0.6212 (ttt) REVERT: W 178 GLN cc_start: 0.8186 (mt0) cc_final: 0.7841 (mt0) REVERT: W 212 GLN cc_start: 0.8754 (mt0) cc_final: 0.8464 (mp10) REVERT: X 208 LYS cc_start: 0.8835 (tptp) cc_final: 0.8480 (tptt) REVERT: X 262 MET cc_start: 0.8399 (mtt) cc_final: 0.8189 (mtm) outliers start: 74 outliers final: 40 residues processed: 706 average time/residue: 0.2291 time to fit residues: 263.4904 Evaluate side-chains 678 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 630 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 401 ASP Chi-restraints excluded: chain 0 residue 479 LEU Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 278 PHE Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 218 LEU Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 255 ASP Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 224 VAL Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 7 residue 116 HIS Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 568 GLU Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 298 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 420 optimal weight: 8.9990 chunk 309 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 336 optimal weight: 0.0060 chunk 425 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 60 GLN 0 291 GLN 1 87 HIS 1 262 ASN 2 223 HIS 6 450 ASN 7 633 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.193614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136742 restraints weight = 43001.050| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.52 r_work: 0.3007 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35866 Z= 0.127 Angle : 0.528 13.366 48474 Z= 0.264 Chirality : 0.040 0.161 5503 Planarity : 0.004 0.048 6101 Dihedral : 7.907 117.618 4888 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 13.82 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.57 (0.13), residues: 4226 helix: 2.22 (0.12), residues: 2004 sheet: 0.07 (0.23), residues: 492 loop : -0.01 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 67 TYR 0.017 0.001 TYR 4 79 PHE 0.022 0.001 PHE 2 269 TRP 0.010 0.001 TRP 4 37 HIS 0.008 0.001 HIS 7 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (35817) covalent geometry : angle 0.51014 / 0.26 (48405) hydrogen bonds : bond 0.03700 / 2.46 ( 1679) hydrogen bonds : angle 4.13266 / 2.94 ( 4788) metal coordination : bond 0.00754 / 0.46 ( 48) metal coordination : angle 3.60746 / 2.06 ( 69) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 652 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7871 (mttt) cc_final: 0.6986 (mmtp) REVERT: 0 78 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7069 (mm-30) REVERT: 0 102 ASP cc_start: 0.8075 (p0) cc_final: 0.7794 (p0) REVERT: 0 131 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6182 (mm-30) REVERT: 0 183 LYS cc_start: 0.7634 (ttmt) cc_final: 0.6934 (mtmm) REVERT: 0 259 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7468 (mtm110) REVERT: 0 357 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8352 (ttmm) REVERT: 0 397 THR cc_start: 0.8449 (t) cc_final: 0.8145 (m) REVERT: 0 413 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: 0 528 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7425 (mm-30) REVERT: 0 620 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8605 (p) REVERT: 0 643 ARG cc_start: 0.7731 (tmm-80) cc_final: 0.7482 (ttp80) REVERT: 0 684 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.7980 (ptm-80) REVERT: 1 11 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8562 (mmmt) REVERT: 1 57 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7401 (pttp) REVERT: 1 252 SER cc_start: 0.8303 (m) cc_final: 0.8080 (t) REVERT: 1 282 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7211 (tm-30) REVERT: 1 302 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: 1 338 ASP cc_start: 0.8238 (t0) cc_final: 0.7523 (t0) REVERT: 1 363 ASP cc_start: 0.8174 (t0) cc_final: 0.7820 (t0) REVERT: 1 421 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.6640 (pt) REVERT: 1 501 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8090 (tttp) REVERT: 1 548 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7454 (tm-30) REVERT: 1 552 MET cc_start: 0.7914 (ttm) cc_final: 0.7623 (mtp) REVERT: 1 581 LYS cc_start: 0.8212 (mttm) cc_final: 0.7613 (ttpt) REVERT: 2 184 ILE cc_start: 0.8400 (mp) cc_final: 0.8096 (mt) REVERT: 2 210 MET cc_start: 0.8079 (mtp) cc_final: 0.7686 (mtp) REVERT: 2 247 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.7921 (mmt90) REVERT: 2 253 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6760 (mmm) REVERT: 2 373 MET cc_start: 0.8373 (ppp) cc_final: 0.8112 (ptt) REVERT: 2 410 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7839 (tmm-80) REVERT: 3 11 ASP cc_start: 0.8626 (t0) cc_final: 0.8086 (t0) REVERT: 3 19 ASP cc_start: 0.7431 (t70) cc_final: 0.6903 (t0) REVERT: 3 37 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8118 (ttp80) REVERT: 3 38 ILE cc_start: 0.8300 (tt) cc_final: 0.7876 (pt) REVERT: 3 40 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7918 (tm-30) REVERT: 3 44 ASP cc_start: 0.8773 (t0) cc_final: 0.8565 (t0) REVERT: 3 46 ILE cc_start: 0.8701 (mt) cc_final: 0.8375 (mm) REVERT: 3 79 GLU cc_start: 0.8659 (mm-30) cc_final: 0.7883 (tp30) REVERT: 3 83 ASP cc_start: 0.7981 (m-30) cc_final: 0.7408 (m-30) REVERT: 3 98 ASP cc_start: 0.8868 (t0) cc_final: 0.8498 (t0) REVERT: 3 111 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7400 (tt0) REVERT: 3 115 ASP cc_start: 0.8187 (t0) cc_final: 0.7918 (t0) REVERT: 3 130 GLU cc_start: 0.8141 (tp30) cc_final: 0.7894 (tp30) REVERT: 4 207 LYS cc_start: 0.8211 (tttt) cc_final: 0.7930 (tmtt) REVERT: 4 281 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7974 (ptp90) REVERT: 4 321 LYS cc_start: 0.7992 (mttt) cc_final: 0.7627 (mtpp) REVERT: 5 27 MET cc_start: 0.6696 (tmm) cc_final: 0.6231 (tmm) REVERT: 6 155 ASP cc_start: 0.7834 (m-30) cc_final: 0.7570 (m-30) REVERT: 6 246 ASP cc_start: 0.8340 (p0) cc_final: 0.8051 (p0) REVERT: 6 252 ASP cc_start: 0.7641 (t0) cc_final: 0.6914 (m-30) REVERT: 6 255 VAL cc_start: 0.8643 (t) cc_final: 0.8363 (t) REVERT: 6 327 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7704 (mtp85) REVERT: 6 348 PHE cc_start: 0.7718 (m-10) cc_final: 0.7468 (m-80) REVERT: 6 357 CYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7273 (m) REVERT: 6 433 LYS cc_start: 0.8542 (mttt) cc_final: 0.7805 (mmtt) REVERT: 7 121 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8475 (pp) REVERT: 7 138 ASP cc_start: 0.7605 (t0) cc_final: 0.7263 (t0) REVERT: 7 156 PHE cc_start: 0.7276 (t80) cc_final: 0.6894 (t80) REVERT: 7 211 ASN cc_start: 0.7567 (m-40) cc_final: 0.7340 (m-40) REVERT: 7 214 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8076 (mtpp) REVERT: 7 244 MET cc_start: 0.6983 (tmm) cc_final: 0.5644 (mtm) REVERT: 7 341 TYR cc_start: 0.8223 (t80) cc_final: 0.7821 (t80) REVERT: 7 355 ASP cc_start: 0.7601 (m-30) cc_final: 0.7395 (m-30) REVERT: 7 362 ILE cc_start: 0.8184 (mm) cc_final: 0.7749 (mt) REVERT: 7 367 GLU cc_start: 0.7272 (tp30) cc_final: 0.6540 (tp30) REVERT: 7 444 GLU cc_start: 0.7334 (mp0) cc_final: 0.7119 (mp0) REVERT: 7 497 MET cc_start: 0.8307 (tpp) cc_final: 0.8041 (tpp) REVERT: 7 568 GLU cc_start: 0.8155 (tp30) cc_final: 0.7565 (tt0) REVERT: 7 578 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7282 (mtp) REVERT: 7 603 ASP cc_start: 0.7832 (m-30) cc_final: 0.7598 (m-30) REVERT: 7 617 GLU cc_start: 0.7863 (tt0) cc_final: 0.7542 (mt-10) REVERT: 7 645 TYR cc_start: 0.7395 (m-80) cc_final: 0.6867 (m-10) REVERT: 7 666 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8088 (mm-30) REVERT: 7 764 LEU cc_start: 0.7957 (mt) cc_final: 0.7028 (mt) REVERT: A 146 MET cc_start: 0.7714 (mmm) cc_final: 0.7438 (mmm) REVERT: A 169 ASN cc_start: 0.8470 (m-40) cc_final: 0.7611 (m110) REVERT: A 226 GLU cc_start: 0.7617 (tt0) cc_final: 0.7270 (tt0) REVERT: A 1398 MET cc_start: 0.6316 (ttt) cc_final: 0.5934 (ttm) REVERT: A 1428 VAL cc_start: 0.8169 (t) cc_final: 0.7966 (t) REVERT: A 1446 ASP cc_start: 0.7633 (t0) cc_final: 0.7038 (p0) REVERT: B 1210 MET cc_start: 0.6852 (mtt) cc_final: 0.6570 (mtt) REVERT: D 31 GLN cc_start: 0.7825 (tp40) cc_final: 0.7447 (tp40) REVERT: D 36 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7895 (mtpp) REVERT: F 104 ASN cc_start: 0.8906 (t0) cc_final: 0.8475 (t0) REVERT: F 122 MET cc_start: 0.4109 (mtt) cc_final: 0.3864 (mtt) REVERT: G 41 LYS cc_start: 0.9040 (tttp) cc_final: 0.8743 (ttpt) REVERT: G 96 GLN cc_start: 0.7861 (pm20) cc_final: 0.7582 (pm20) REVERT: W 45 GLN cc_start: 0.8503 (tm-30) cc_final: 0.7953 (tm-30) REVERT: W 123 MET cc_start: 0.6588 (ttp) cc_final: 0.6219 (ttt) REVERT: W 178 GLN cc_start: 0.8267 (mt0) cc_final: 0.7828 (mt0) REVERT: W 212 GLN cc_start: 0.8802 (mt0) cc_final: 0.8490 (mp10) REVERT: X 208 LYS cc_start: 0.8819 (tptp) cc_final: 0.8451 (tptt) REVERT: X 262 MET cc_start: 0.8264 (mtt) cc_final: 0.8027 (mtm) outliers start: 73 outliers final: 50 residues processed: 688 average time/residue: 0.2227 time to fit residues: 249.9469 Evaluate side-chains 681 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 622 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 413 GLU Chi-restraints excluded: chain 0 residue 451 GLU Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 647 ARG Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 421 ILE Chi-restraints excluded: chain 1 residue 578 THR Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 272 THR Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 3 residue 104 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 335 PHE Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 6 residue 450 ASN Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 194 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 305 optimal weight: 1.9990 chunk 166 optimal weight: 50.0000 chunk 427 optimal weight: 2.9990 chunk 423 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 397 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 208 optimal weight: 0.0870 chunk 415 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 291 GLN 2 223 HIS 2 389 ASN 7 738 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.186097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126976 restraints weight = 42947.653| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.56 r_work: 0.3058 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 35866 Z= 0.289 Angle : 0.608 11.104 48474 Z= 0.307 Chirality : 0.044 0.206 5503 Planarity : 0.004 0.057 6101 Dihedral : 8.073 118.501 4888 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.51 % Allowed : 14.46 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.35 (0.13), residues: 4226 helix: 2.03 (0.12), residues: 2006 sheet: -0.09 (0.23), residues: 500 loop : -0.09 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 68 TYR 0.022 0.002 TYR 0 208 PHE 0.031 0.002 PHE A 22 TRP 0.014 0.002 TRP 2 65 HIS 0.008 0.001 HIS 6 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.29 (35817) covalent geometry : angle 0.59197 / 0.31 (48405) hydrogen bonds : bond 0.04412 / 2.94 ( 1679) hydrogen bonds : angle 4.27851 / 3.04 ( 4788) metal coordination : bond 0.01172 / 0.65 ( 48) metal coordination : angle 3.68997 / 2.26 ( 69) Misc. bond : bond 0.00126 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 663 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.8001 (mttt) cc_final: 0.7430 (mmtp) REVERT: 0 41 GLU cc_start: 0.8225 (tt0) cc_final: 0.8003 (tt0) REVERT: 0 78 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7360 (mm-30) REVERT: 0 87 GLU cc_start: 0.7934 (tt0) cc_final: 0.7707 (tt0) REVERT: 0 102 ASP cc_start: 0.8057 (p0) cc_final: 0.7770 (p0) REVERT: 0 131 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6394 (mm-30) REVERT: 0 183 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7178 (mtmm) REVERT: 0 255 ASP cc_start: 0.7816 (t0) cc_final: 0.7219 (t0) REVERT: 0 259 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7665 (mtt-85) REVERT: 0 397 THR cc_start: 0.8660 (t) cc_final: 0.8370 (m) REVERT: 0 528 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7616 (mm-30) REVERT: 0 584 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7492 (tt0) REVERT: 0 620 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8623 (p) REVERT: 0 643 ARG cc_start: 0.7919 (tmm-80) cc_final: 0.7579 (ttp80) REVERT: 0 684 ARG cc_start: 0.8595 (ttp-170) cc_final: 0.8271 (ttp80) REVERT: 1 11 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8575 (mmmt) REVERT: 1 57 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7579 (pttp) REVERT: 1 252 SER cc_start: 0.8442 (m) cc_final: 0.8232 (t) REVERT: 1 282 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7275 (tm-30) REVERT: 1 302 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6397 (tmm) REVERT: 1 326 ASP cc_start: 0.7102 (m-30) cc_final: 0.6745 (t70) REVERT: 1 338 ASP cc_start: 0.8343 (t0) cc_final: 0.7541 (t0) REVERT: 1 421 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.6908 (pt) REVERT: 1 501 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8168 (tttp) REVERT: 1 548 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7510 (tm-30) REVERT: 1 581 LYS cc_start: 0.8221 (mttm) cc_final: 0.7630 (ttpt) REVERT: 2 184 ILE cc_start: 0.8590 (mp) cc_final: 0.8290 (mt) REVERT: 2 210 MET cc_start: 0.8193 (mtp) cc_final: 0.7819 (mtp) REVERT: 2 247 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.7913 (mmt90) REVERT: 2 253 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7075 (mmm) REVERT: 2 373 MET cc_start: 0.8503 (ppp) cc_final: 0.8055 (ptt) REVERT: 3 38 ILE cc_start: 0.8527 (tt) cc_final: 0.8045 (pt) REVERT: 3 40 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7967 (tm-30) REVERT: 3 44 ASP cc_start: 0.8755 (t0) cc_final: 0.8539 (t0) REVERT: 3 46 ILE cc_start: 0.8811 (mt) cc_final: 0.8479 (mm) REVERT: 3 111 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7569 (tt0) REVERT: 4 207 LYS cc_start: 0.8393 (tttt) cc_final: 0.8158 (tmtt) REVERT: 4 281 ARG cc_start: 0.8336 (ptp90) cc_final: 0.7927 (ptp90) REVERT: 4 321 LYS cc_start: 0.8116 (mttt) cc_final: 0.7747 (mtpp) REVERT: 5 27 MET cc_start: 0.6769 (tmm) cc_final: 0.6306 (tmm) REVERT: 5 54 LEU cc_start: 0.8146 (mt) cc_final: 0.7883 (mm) REVERT: 6 155 ASP cc_start: 0.7882 (m-30) cc_final: 0.7641 (m-30) REVERT: 6 246 ASP cc_start: 0.8432 (p0) cc_final: 0.8046 (p0) REVERT: 6 252 ASP cc_start: 0.7796 (t0) cc_final: 0.7091 (m-30) REVERT: 6 255 VAL cc_start: 0.8839 (t) cc_final: 0.8594 (t) REVERT: 6 299 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7720 (mm-30) REVERT: 6 348 PHE cc_start: 0.7962 (m-10) cc_final: 0.7643 (m-80) REVERT: 6 357 CYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7388 (m) REVERT: 6 433 LYS cc_start: 0.8541 (mttt) cc_final: 0.7869 (mmtt) REVERT: 7 118 PHE cc_start: 0.8898 (m-80) cc_final: 0.8655 (m-80) REVERT: 7 121 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8581 (pp) REVERT: 7 138 ASP cc_start: 0.7712 (t0) cc_final: 0.7280 (t0) REVERT: 7 211 ASN cc_start: 0.7605 (m-40) cc_final: 0.7393 (m-40) REVERT: 7 214 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8165 (mtpp) REVERT: 7 341 TYR cc_start: 0.8347 (t80) cc_final: 0.8019 (t80) REVERT: 7 355 ASP cc_start: 0.7638 (m-30) cc_final: 0.7391 (m-30) REVERT: 7 362 ILE cc_start: 0.8229 (mm) cc_final: 0.7850 (mt) REVERT: 7 367 GLU cc_start: 0.7380 (tp30) cc_final: 0.6702 (tp30) REVERT: 7 444 GLU cc_start: 0.7407 (mp0) cc_final: 0.7184 (mp0) REVERT: 7 490 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8702 (t) REVERT: 7 568 GLU cc_start: 0.8249 (tp30) cc_final: 0.7641 (tt0) REVERT: 7 578 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: 7 645 TYR cc_start: 0.7477 (m-80) cc_final: 0.6915 (m-10) REVERT: 7 666 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8184 (mm-30) REVERT: 7 694 LYS cc_start: 0.8583 (tppt) cc_final: 0.8303 (mmtt) REVERT: A 146 MET cc_start: 0.7832 (mmm) cc_final: 0.7562 (mmm) REVERT: A 169 ASN cc_start: 0.8588 (m-40) cc_final: 0.7812 (m110) REVERT: A 226 GLU cc_start: 0.7696 (tt0) cc_final: 0.7373 (tt0) REVERT: A 500 GLU cc_start: 0.7615 (tt0) cc_final: 0.7291 (tt0) REVERT: A 1398 MET cc_start: 0.6517 (ttt) cc_final: 0.6110 (ttm) REVERT: A 1446 ASP cc_start: 0.7693 (t0) cc_final: 0.7138 (p0) REVERT: B 1210 MET cc_start: 0.6854 (mtt) cc_final: 0.6604 (mtt) REVERT: D 31 GLN cc_start: 0.7993 (tp40) cc_final: 0.7658 (tp40) REVERT: D 36 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8034 (mtpp) REVERT: F 104 ASN cc_start: 0.8982 (t0) cc_final: 0.8557 (t0) REVERT: F 122 MET cc_start: 0.4137 (mtt) cc_final: 0.3914 (mtt) REVERT: G 23 LYS cc_start: 0.8349 (mttm) cc_final: 0.7999 (mttp) REVERT: G 41 LYS cc_start: 0.9043 (tttp) cc_final: 0.8774 (tttt) REVERT: G 96 GLN cc_start: 0.8007 (pm20) cc_final: 0.7789 (pm20) REVERT: W 45 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8044 (tm-30) REVERT: W 123 MET cc_start: 0.6644 (ttp) cc_final: 0.6310 (ttt) REVERT: W 174 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7875 (ttp-110) REVERT: W 178 GLN cc_start: 0.8333 (mt0) cc_final: 0.7914 (mt0) REVERT: W 212 GLN cc_start: 0.8790 (mt0) cc_final: 0.8517 (mp10) REVERT: X 208 LYS cc_start: 0.8866 (tptp) cc_final: 0.8494 (tptt) REVERT: X 262 MET cc_start: 0.8497 (mtt) cc_final: 0.8265 (mtm) outliers start: 98 outliers final: 70 residues processed: 713 average time/residue: 0.2280 time to fit residues: 264.3592 Evaluate side-chains 706 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 627 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 253 THR Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 451 GLU Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 647 ARG Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 1 residue 421 ILE Chi-restraints excluded: chain 1 residue 578 THR Chi-restraints excluded: chain 1 residue 590 ILE Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 272 THR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 3 residue 70 THR Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 104 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 241 THR Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 295 THR Chi-restraints excluded: chain 6 residue 305 VAL Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 335 PHE Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 6 residue 368 LEU Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 7 residue 360 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 415 VAL Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 221 ILE Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 114 optimal weight: 3.9990 chunk 419 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 chunk 310 optimal weight: 0.9990 chunk 421 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 424 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 60 GLN 0 291 GLN 2 223 HIS 4 226 GLN 7 584 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.186070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126606 restraints weight = 42981.232| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.58 r_work: 0.2948 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35866 Z= 0.185 Angle : 0.574 12.124 48474 Z= 0.288 Chirality : 0.042 0.160 5503 Planarity : 0.004 0.053 6101 Dihedral : 8.097 118.757 4888 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.30 % Allowed : 15.12 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.35 (0.13), residues: 4226 helix: 2.04 (0.12), residues: 1999 sheet: -0.12 (0.23), residues: 499 loop : -0.09 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 254 TYR 0.019 0.001 TYR 4 79 PHE 0.026 0.001 PHE 2 224 TRP 0.014 0.001 TRP 2 65 HIS 0.008 0.001 HIS 7 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (35817) covalent geometry : angle 0.55809 / 0.29 (48405) hydrogen bonds : bond 0.03999 / 2.66 ( 1679) hydrogen bonds : angle 4.19474 / 2.99 ( 4788) metal coordination : bond 0.00917 / 0.54 ( 48) metal coordination : angle 3.60570 / 2.20 ( 69) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 632 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7942 (mttt) cc_final: 0.7360 (mmtp) REVERT: 0 78 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7617 (mm-30) REVERT: 0 87 GLU cc_start: 0.8144 (tt0) cc_final: 0.7917 (tt0) REVERT: 0 102 ASP cc_start: 0.8255 (p0) cc_final: 0.7963 (p0) REVERT: 0 131 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6359 (mm-30) REVERT: 0 183 LYS cc_start: 0.7596 (ttmt) cc_final: 0.6869 (mtmm) REVERT: 0 255 ASP cc_start: 0.7887 (t0) cc_final: 0.7359 (t0) REVERT: 0 259 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7760 (mtt-85) REVERT: 0 397 THR cc_start: 0.8723 (t) cc_final: 0.8428 (m) REVERT: 0 528 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7678 (mm-30) REVERT: 0 544 TYR cc_start: 0.8877 (t80) cc_final: 0.8616 (t80) REVERT: 0 620 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8626 (p) REVERT: 0 643 ARG cc_start: 0.7888 (tmm-80) cc_final: 0.7543 (ttp80) REVERT: 0 684 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8424 (ttp80) REVERT: 1 11 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8547 (mmmt) REVERT: 1 57 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7504 (pttp) REVERT: 1 252 SER cc_start: 0.8397 (m) cc_final: 0.8151 (t) REVERT: 1 282 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7335 (tm-30) REVERT: 1 302 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6598 (tmm) REVERT: 1 326 ASP cc_start: 0.7065 (m-30) cc_final: 0.6670 (t70) REVERT: 1 338 ASP cc_start: 0.8434 (t0) cc_final: 0.8139 (t0) REVERT: 1 363 ASP cc_start: 0.8276 (t0) cc_final: 0.7910 (t0) REVERT: 1 421 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.6794 (pt) REVERT: 1 501 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8115 (tttp) REVERT: 1 548 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7593 (tm-30) REVERT: 1 581 LYS cc_start: 0.8237 (mttm) cc_final: 0.7638 (ttmt) REVERT: 2 85 HIS cc_start: 0.8000 (m90) cc_final: 0.7586 (m90) REVERT: 2 184 ILE cc_start: 0.8564 (mp) cc_final: 0.8212 (mt) REVERT: 2 210 MET cc_start: 0.8199 (mtp) cc_final: 0.7872 (mtp) REVERT: 2 247 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8221 (mtp85) REVERT: 2 253 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6822 (mmm) REVERT: 2 373 MET cc_start: 0.8620 (ppp) cc_final: 0.8326 (ptt) REVERT: 2 410 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7885 (ttp80) REVERT: 2 445 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8170 (tp40) REVERT: 3 21 TYR cc_start: 0.8360 (t80) cc_final: 0.8107 (t80) REVERT: 3 38 ILE cc_start: 0.8365 (tt) cc_final: 0.7949 (pt) REVERT: 3 40 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8013 (tm-30) REVERT: 3 44 ASP cc_start: 0.8810 (t0) cc_final: 0.8609 (t0) REVERT: 3 46 ILE cc_start: 0.8709 (mt) cc_final: 0.8389 (mm) REVERT: 4 207 LYS cc_start: 0.8362 (tttt) cc_final: 0.8083 (tmtt) REVERT: 4 281 ARG cc_start: 0.8474 (ptp90) cc_final: 0.8036 (ptp90) REVERT: 4 321 LYS cc_start: 0.8064 (mttt) cc_final: 0.7657 (mtpp) REVERT: 5 27 MET cc_start: 0.6553 (tmm) cc_final: 0.6221 (tmm) REVERT: 5 54 LEU cc_start: 0.8069 (mt) cc_final: 0.7813 (mm) REVERT: 6 155 ASP cc_start: 0.8024 (m-30) cc_final: 0.7777 (m-30) REVERT: 6 246 ASP cc_start: 0.8593 (p0) cc_final: 0.8224 (p0) REVERT: 6 252 ASP cc_start: 0.7786 (t0) cc_final: 0.7065 (m-30) REVERT: 6 255 VAL cc_start: 0.8691 (t) cc_final: 0.8439 (t) REVERT: 6 348 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: 6 357 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7579 (m) REVERT: 6 369 MET cc_start: 0.7660 (ttp) cc_final: 0.7426 (ttp) REVERT: 6 433 LYS cc_start: 0.8538 (mttt) cc_final: 0.7785 (mmtt) REVERT: 6 446 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6843 (mt-10) REVERT: 7 118 PHE cc_start: 0.8897 (m-80) cc_final: 0.8623 (m-80) REVERT: 7 121 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8489 (pp) REVERT: 7 138 ASP cc_start: 0.7900 (t0) cc_final: 0.7525 (t0) REVERT: 7 211 ASN cc_start: 0.7617 (m-40) cc_final: 0.7389 (m-40) REVERT: 7 214 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8067 (mtpp) REVERT: 7 244 MET cc_start: 0.7132 (tmm) cc_final: 0.5427 (mtm) REVERT: 7 341 TYR cc_start: 0.8386 (t80) cc_final: 0.8068 (t80) REVERT: 7 343 PHE cc_start: 0.7962 (p90) cc_final: 0.7630 (p90) REVERT: 7 362 ILE cc_start: 0.8226 (mm) cc_final: 0.7834 (mt) REVERT: 7 367 GLU cc_start: 0.7350 (tp30) cc_final: 0.6702 (tp30) REVERT: 7 444 GLU cc_start: 0.7615 (mp0) cc_final: 0.7286 (mp0) REVERT: 7 497 MET cc_start: 0.8567 (tpp) cc_final: 0.8293 (tpp) REVERT: 7 568 GLU cc_start: 0.8221 (tp30) cc_final: 0.7657 (tt0) REVERT: 7 578 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7488 (mtp) REVERT: 7 617 GLU cc_start: 0.8030 (tt0) cc_final: 0.7603 (mt-10) REVERT: 7 645 TYR cc_start: 0.7486 (m-80) cc_final: 0.6842 (m-10) REVERT: 7 666 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8340 (mm-30) REVERT: 7 694 LYS cc_start: 0.8545 (tppt) cc_final: 0.8230 (mmtt) REVERT: 7 764 LEU cc_start: 0.8064 (mt) cc_final: 0.7234 (mt) REVERT: A 146 MET cc_start: 0.7896 (mmm) cc_final: 0.7589 (mmm) REVERT: A 169 ASN cc_start: 0.8567 (m-40) cc_final: 0.7786 (m110) REVERT: A 226 GLU cc_start: 0.7902 (tt0) cc_final: 0.7534 (tt0) REVERT: A 500 GLU cc_start: 0.7557 (tt0) cc_final: 0.7311 (tt0) REVERT: A 1398 MET cc_start: 0.6558 (ttt) cc_final: 0.6058 (ttm) REVERT: A 1446 ASP cc_start: 0.8001 (t0) cc_final: 0.7118 (p0) REVERT: A 1450 LEU cc_start: 0.8096 (mp) cc_final: 0.7812 (mp) REVERT: B 1210 MET cc_start: 0.6840 (mtt) cc_final: 0.6590 (mtt) REVERT: D 31 GLN cc_start: 0.8119 (tp40) cc_final: 0.7732 (tp40) REVERT: D 36 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8006 (mtpp) REVERT: F 122 MET cc_start: 0.4117 (mtt) cc_final: 0.3853 (mtt) REVERT: G 23 LYS cc_start: 0.8335 (mttm) cc_final: 0.7995 (mttp) REVERT: G 41 LYS cc_start: 0.9141 (tttp) cc_final: 0.8856 (tttt) REVERT: G 96 GLN cc_start: 0.7992 (pm20) cc_final: 0.7720 (pm20) REVERT: G 115 MET cc_start: 0.8719 (mtp) cc_final: 0.8438 (mtm) REVERT: W 45 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8078 (tm-30) REVERT: W 123 MET cc_start: 0.6611 (ttp) cc_final: 0.6208 (ttt) REVERT: W 174 ARG cc_start: 0.8494 (mtm180) cc_final: 0.7923 (ttp-110) REVERT: W 178 GLN cc_start: 0.8441 (mt0) cc_final: 0.7959 (mt0) REVERT: W 212 GLN cc_start: 0.8909 (mt0) cc_final: 0.8596 (mp10) REVERT: X 208 LYS cc_start: 0.8827 (tptp) cc_final: 0.8408 (tptt) REVERT: X 262 MET cc_start: 0.8485 (mtt) cc_final: 0.8245 (mtm) outliers start: 90 outliers final: 60 residues processed: 678 average time/residue: 0.2299 time to fit residues: 252.2597 Evaluate side-chains 690 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 620 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 253 THR Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 647 ARG Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 1 residue 421 ILE Chi-restraints excluded: chain 1 residue 578 THR Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 249 MET Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 272 THR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 445 GLN Chi-restraints excluded: chain 3 residue 70 THR Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 104 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 335 PHE Chi-restraints excluded: chain 6 residue 348 PHE Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 378 ARG Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 99 optimal weight: 7.9990 chunk 401 optimal weight: 0.0060 chunk 45 optimal weight: 0.6980 chunk 345 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 chunk 374 optimal weight: 0.4980 chunk 334 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 60 GLN 1 554 HIS ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 161 ASN 4 311 GLN 7 127 HIS ** 7 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN 7 738 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.189198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130960 restraints weight = 43089.178| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.55 r_work: 0.2973 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35866 Z= 0.132 Angle : 0.554 12.594 48474 Z= 0.276 Chirality : 0.040 0.159 5503 Planarity : 0.004 0.052 6101 Dihedral : 8.041 118.176 4888 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 15.56 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.42 (0.13), residues: 4226 helix: 2.09 (0.12), residues: 2005 sheet: -0.09 (0.23), residues: 507 loop : -0.05 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 193 TYR 0.019 0.001 TYR 4 79 PHE 0.021 0.001 PHE 2 269 TRP 0.015 0.001 TRP X 214 HIS 0.008 0.001 HIS 7 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (35817) covalent geometry : angle 0.53843 / 0.27 (48405) hydrogen bonds : bond 0.03642 / 2.42 ( 1679) hydrogen bonds : angle 4.10039 / 2.92 ( 4788) metal coordination : bond 0.00748 / 0.47 ( 48) metal coordination : angle 3.54276 / 2.08 ( 69) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 615 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7887 (mttt) cc_final: 0.7292 (mmtp) REVERT: 0 78 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7116 (mm-30) REVERT: 0 87 GLU cc_start: 0.7896 (tt0) cc_final: 0.7631 (tt0) REVERT: 0 102 ASP cc_start: 0.8067 (p0) cc_final: 0.7750 (p0) REVERT: 0 131 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6202 (mm-30) REVERT: 0 183 LYS cc_start: 0.7617 (ttmt) cc_final: 0.6904 (mtmm) REVERT: 0 255 ASP cc_start: 0.7738 (t0) cc_final: 0.7077 (t0) REVERT: 0 259 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7538 (mtt-85) REVERT: 0 291 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7915 (mm110) REVERT: 0 397 THR cc_start: 0.8572 (t) cc_final: 0.8264 (m) REVERT: 0 528 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7412 (mm-30) REVERT: 0 620 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8589 (p) REVERT: 0 643 ARG cc_start: 0.7745 (tmm-80) cc_final: 0.7457 (ttp80) REVERT: 0 684 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8289 (ttp80) REVERT: 1 11 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8542 (mmmt) REVERT: 1 57 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7319 (pttp) REVERT: 1 252 SER cc_start: 0.8402 (m) cc_final: 0.8156 (t) REVERT: 1 262 ASN cc_start: 0.7460 (m110) cc_final: 0.7115 (m110) REVERT: 1 282 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7243 (tm-30) REVERT: 1 302 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6403 (tmm) REVERT: 1 326 ASP cc_start: 0.7117 (m-30) cc_final: 0.6703 (t70) REVERT: 1 338 ASP cc_start: 0.8336 (t0) cc_final: 0.7844 (t70) REVERT: 1 363 ASP cc_start: 0.8189 (t0) cc_final: 0.7862 (t0) REVERT: 1 386 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8086 (tp) REVERT: 1 421 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.6667 (pt) REVERT: 1 501 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8073 (tttp) REVERT: 1 548 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7543 (tm-30) REVERT: 1 581 LYS cc_start: 0.8184 (mttm) cc_final: 0.7616 (ttmt) REVERT: 2 85 HIS cc_start: 0.7853 (m90) cc_final: 0.7496 (m90) REVERT: 2 184 ILE cc_start: 0.8512 (mp) cc_final: 0.8200 (mt) REVERT: 2 210 MET cc_start: 0.8142 (mtp) cc_final: 0.7784 (mtp) REVERT: 2 247 ARG cc_start: 0.8440 (mtt-85) cc_final: 0.7900 (mmt90) REVERT: 2 253 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6881 (mmm) REVERT: 2 373 MET cc_start: 0.8466 (ppp) cc_final: 0.8193 (ptt) REVERT: 2 445 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8094 (tp40) REVERT: 3 37 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8079 (ttp80) REVERT: 3 38 ILE cc_start: 0.8377 (tt) cc_final: 0.7964 (pt) REVERT: 3 46 ILE cc_start: 0.8685 (mt) cc_final: 0.8355 (mm) REVERT: 4 207 LYS cc_start: 0.8253 (tttt) cc_final: 0.7974 (tmtt) REVERT: 4 281 ARG cc_start: 0.8444 (ptp90) cc_final: 0.8035 (ptp90) REVERT: 4 321 LYS cc_start: 0.8049 (mttt) cc_final: 0.7661 (mtpp) REVERT: 5 54 LEU cc_start: 0.8074 (mt) cc_final: 0.7815 (mm) REVERT: 6 155 ASP cc_start: 0.7893 (m-30) cc_final: 0.7588 (m-30) REVERT: 6 246 ASP cc_start: 0.8388 (p0) cc_final: 0.8002 (p0) REVERT: 6 252 ASP cc_start: 0.7614 (t0) cc_final: 0.6905 (m-30) REVERT: 6 255 VAL cc_start: 0.8665 (t) cc_final: 0.8395 (t) REVERT: 6 348 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: 6 357 CYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7267 (m) REVERT: 6 384 MET cc_start: 0.8054 (tpp) cc_final: 0.6961 (ptp) REVERT: 6 433 LYS cc_start: 0.8540 (mttt) cc_final: 0.7800 (mmtt) REVERT: 7 118 PHE cc_start: 0.8870 (m-80) cc_final: 0.8591 (m-80) REVERT: 7 121 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8451 (pp) REVERT: 7 138 ASP cc_start: 0.7689 (t0) cc_final: 0.7309 (t0) REVERT: 7 156 PHE cc_start: 0.7332 (t80) cc_final: 0.6913 (t80) REVERT: 7 211 ASN cc_start: 0.7579 (m-40) cc_final: 0.7356 (m-40) REVERT: 7 214 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8075 (mtpp) REVERT: 7 244 MET cc_start: 0.7209 (tmm) cc_final: 0.5601 (mtm) REVERT: 7 341 TYR cc_start: 0.8229 (t80) cc_final: 0.7868 (t80) REVERT: 7 362 ILE cc_start: 0.8163 (mm) cc_final: 0.7782 (mt) REVERT: 7 367 GLU cc_start: 0.7200 (tp30) cc_final: 0.6508 (tp30) REVERT: 7 378 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6738 (mtm-85) REVERT: 7 444 GLU cc_start: 0.7455 (mp0) cc_final: 0.7154 (mp0) REVERT: 7 497 MET cc_start: 0.8387 (tpp) cc_final: 0.8119 (tpp) REVERT: 7 564 GLU cc_start: 0.8382 (tp30) cc_final: 0.7973 (tp30) REVERT: 7 568 GLU cc_start: 0.8112 (tp30) cc_final: 0.7518 (tt0) REVERT: 7 578 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: 7 621 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7567 (mmtm) REVERT: 7 645 TYR cc_start: 0.7410 (m-80) cc_final: 0.6864 (m-10) REVERT: 7 666 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8157 (mm-30) REVERT: 7 694 LYS cc_start: 0.8517 (tppt) cc_final: 0.8213 (mmtt) REVERT: 7 729 GLN cc_start: 0.8072 (mm110) cc_final: 0.7807 (mm110) REVERT: 7 764 LEU cc_start: 0.7980 (mt) cc_final: 0.7085 (mt) REVERT: A 146 MET cc_start: 0.7802 (mmm) cc_final: 0.7527 (mmm) REVERT: A 169 ASN cc_start: 0.8493 (m-40) cc_final: 0.7631 (m110) REVERT: A 226 GLU cc_start: 0.7660 (tt0) cc_final: 0.7307 (tt0) REVERT: A 1398 MET cc_start: 0.6413 (ttt) cc_final: 0.5955 (ttm) REVERT: A 1446 ASP cc_start: 0.7702 (t0) cc_final: 0.6903 (p0) REVERT: A 1450 LEU cc_start: 0.7937 (mp) cc_final: 0.7710 (mp) REVERT: B 1210 MET cc_start: 0.6940 (mtt) cc_final: 0.6640 (mtt) REVERT: D 31 GLN cc_start: 0.7936 (tp40) cc_final: 0.7580 (tp40) REVERT: D 36 LYS cc_start: 0.8474 (mmtt) cc_final: 0.7986 (mtpp) REVERT: F 122 MET cc_start: 0.4114 (mtt) cc_final: 0.3846 (mtt) REVERT: G 41 LYS cc_start: 0.9052 (tttp) cc_final: 0.8758 (tttt) REVERT: G 96 GLN cc_start: 0.7902 (pm20) cc_final: 0.7672 (pm20) REVERT: G 115 MET cc_start: 0.8691 (mtp) cc_final: 0.8475 (mtm) REVERT: W 45 GLN cc_start: 0.8521 (tm-30) cc_final: 0.7961 (tm-30) REVERT: W 123 MET cc_start: 0.6629 (ttp) cc_final: 0.6258 (ttt) REVERT: W 174 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7858 (ttp-110) REVERT: W 178 GLN cc_start: 0.8342 (mt0) cc_final: 0.7865 (mt0) REVERT: W 212 GLN cc_start: 0.8786 (mt0) cc_final: 0.8482 (mp10) REVERT: X 208 LYS cc_start: 0.8816 (tptp) cc_final: 0.8401 (tptt) REVERT: X 262 MET cc_start: 0.8383 (mtt) cc_final: 0.8155 (mtm) outliers start: 84 outliers final: 59 residues processed: 658 average time/residue: 0.2274 time to fit residues: 243.7233 Evaluate side-chains 677 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 606 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 647 ARG Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 1 residue 421 ILE Chi-restraints excluded: chain 1 residue 437 LEU Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 249 MET Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 272 THR Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 445 GLN Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 104 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 335 PHE Chi-restraints excluded: chain 6 residue 348 PHE Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 378 ARG Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 409 optimal weight: 9.9990 chunk 418 optimal weight: 2.9990 chunk 309 optimal weight: 0.0030 chunk 299 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 426 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 223 HIS ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 127 HIS ** 7 584 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 = 0.4061 r_free = 0.4061 target = 0.186547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128045 restraints weight = 42942.868| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.71 r_work: 0.3059 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 35866 Z= 0.216 Angle : 0.596 12.017 48474 Z= 0.298 Chirality : 0.042 0.178 5503 Planarity : 0.004 0.091 6101 Dihedral : 8.090 118.284 4888 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.10 % Allowed : 15.84 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.31 (0.13), residues: 4226 helix: 2.01 (0.12), residues: 2006 sheet: -0.16 (0.23), residues: 508 loop : -0.11 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG W 193 TYR 0.019 0.001 TYR 7 581 PHE 0.030 0.002 PHE 2 269 TRP 0.015 0.002 TRP X 214 HIS 0.008 0.001 HIS 7 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (35817) covalent geometry : angle 0.58062 / 0.30 (48405) hydrogen bonds : bond 0.03995 / 2.66 ( 1679) hydrogen bonds : angle 4.16559 / 2.97 ( 4788) metal coordination : bond 0.00932 / 0.52 ( 48) metal coordination : angle 3.58142 / 2.16 ( 69) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 614 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7997 (mttt) cc_final: 0.7434 (mmtp) REVERT: 0 78 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7334 (mm-30) REVERT: 0 102 ASP cc_start: 0.8022 (p0) cc_final: 0.7721 (p0) REVERT: 0 131 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6378 (mm-30) REVERT: 0 183 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7085 (mtmm) REVERT: 0 255 ASP cc_start: 0.7894 (t0) cc_final: 0.7302 (t0) REVERT: 0 259 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7682 (mtt-85) REVERT: 0 397 THR cc_start: 0.8631 (t) cc_final: 0.8334 (m) REVERT: 0 528 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7529 (mm-30) REVERT: 0 620 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8518 (p) REVERT: 0 643 ARG cc_start: 0.7901 (tmm-80) cc_final: 0.7524 (ttp80) REVERT: 0 684 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8286 (ttp80) REVERT: 1 11 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8560 (mmmt) REVERT: 1 57 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7448 (pttp) REVERT: 1 252 SER cc_start: 0.8467 (m) cc_final: 0.8242 (t) REVERT: 1 262 ASN cc_start: 0.7463 (m110) cc_final: 0.7125 (m110) REVERT: 1 282 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7273 (tm-30) REVERT: 1 302 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6346 (tmm) REVERT: 1 326 ASP cc_start: 0.7095 (m-30) cc_final: 0.6713 (t70) REVERT: 1 338 ASP cc_start: 0.8376 (t0) cc_final: 0.7870 (t70) REVERT: 1 363 ASP cc_start: 0.8235 (t0) cc_final: 0.7912 (t0) REVERT: 1 421 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.6858 (pt) REVERT: 1 501 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8130 (tttp) REVERT: 1 548 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7519 (tm-30) REVERT: 1 581 LYS cc_start: 0.8187 (mttm) cc_final: 0.7633 (ttmt) REVERT: 2 85 HIS cc_start: 0.7932 (m90) cc_final: 0.7568 (m90) REVERT: 2 184 ILE cc_start: 0.8662 (mp) cc_final: 0.8372 (mt) REVERT: 2 210 MET cc_start: 0.8257 (mtp) cc_final: 0.7876 (mtm) REVERT: 2 247 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.7920 (mmt90) REVERT: 2 253 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7092 (mmm) REVERT: 2 373 MET cc_start: 0.8494 (ppp) cc_final: 0.8116 (ptt) REVERT: 2 385 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7057 (ttm170) REVERT: 2 445 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8209 (tp40) REVERT: 3 37 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8164 (ttp80) REVERT: 3 38 ILE cc_start: 0.8555 (tt) cc_final: 0.8099 (pt) REVERT: 3 46 ILE cc_start: 0.8804 (mt) cc_final: 0.8458 (mm) REVERT: 4 207 LYS cc_start: 0.8333 (tttt) cc_final: 0.8051 (tmtt) REVERT: 4 281 ARG cc_start: 0.8402 (ptp90) cc_final: 0.8015 (ptp90) REVERT: 4 321 LYS cc_start: 0.8097 (mttt) cc_final: 0.7703 (mtpp) REVERT: 5 54 LEU cc_start: 0.8177 (mt) cc_final: 0.7909 (mm) REVERT: 6 155 ASP cc_start: 0.7915 (m-30) cc_final: 0.7655 (m-30) REVERT: 6 246 ASP cc_start: 0.8489 (p0) cc_final: 0.8107 (p0) REVERT: 6 252 ASP cc_start: 0.7759 (t0) cc_final: 0.7086 (m-30) REVERT: 6 255 VAL cc_start: 0.8813 (t) cc_final: 0.8551 (t) REVERT: 6 348 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: 6 357 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7372 (m) REVERT: 6 369 MET cc_start: 0.7718 (ttp) cc_final: 0.7482 (ttp) REVERT: 6 384 MET cc_start: 0.8167 (tpp) cc_final: 0.7113 (ptp) REVERT: 6 433 LYS cc_start: 0.8552 (mttt) cc_final: 0.7873 (mmtt) REVERT: 7 121 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8570 (pp) REVERT: 7 138 ASP cc_start: 0.7722 (t0) cc_final: 0.7264 (t0) REVERT: 7 211 ASN cc_start: 0.7623 (m-40) cc_final: 0.7415 (m-40) REVERT: 7 214 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8145 (mtpp) REVERT: 7 244 MET cc_start: 0.7230 (tmm) cc_final: 0.5615 (mtm) REVERT: 7 341 TYR cc_start: 0.8305 (t80) cc_final: 0.7971 (t80) REVERT: 7 343 PHE cc_start: 0.8024 (p90) cc_final: 0.7676 (p90) REVERT: 7 362 ILE cc_start: 0.8231 (mm) cc_final: 0.7876 (mt) REVERT: 7 367 GLU cc_start: 0.7425 (tp30) cc_final: 0.6730 (tp30) REVERT: 7 444 GLU cc_start: 0.7509 (mp0) cc_final: 0.7263 (mp0) REVERT: 7 497 MET cc_start: 0.8482 (tpp) cc_final: 0.8241 (tpp) REVERT: 7 564 GLU cc_start: 0.8424 (tp30) cc_final: 0.8048 (tp30) REVERT: 7 568 GLU cc_start: 0.8209 (tp30) cc_final: 0.7642 (tt0) REVERT: 7 578 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7541 (mtp) REVERT: 7 617 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7530 (mt-10) REVERT: 7 621 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7697 (mmtm) REVERT: 7 645 TYR cc_start: 0.7491 (m-80) cc_final: 0.6966 (m-10) REVERT: 7 666 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8242 (mm-30) REVERT: 7 729 GLN cc_start: 0.8086 (mm110) cc_final: 0.7835 (mm110) REVERT: 7 764 LEU cc_start: 0.7990 (mt) cc_final: 0.7050 (mt) REVERT: A 146 MET cc_start: 0.7863 (mmm) cc_final: 0.7597 (mmm) REVERT: A 169 ASN cc_start: 0.8604 (m-40) cc_final: 0.7812 (m110) REVERT: A 226 GLU cc_start: 0.7725 (tt0) cc_final: 0.7398 (tt0) REVERT: A 1398 MET cc_start: 0.6546 (ttt) cc_final: 0.6105 (ttm) REVERT: A 1446 ASP cc_start: 0.7698 (t0) cc_final: 0.7027 (p0) REVERT: B 1210 MET cc_start: 0.6928 (mtt) cc_final: 0.6672 (mtt) REVERT: D 31 GLN cc_start: 0.8014 (tp40) cc_final: 0.7686 (tp40) REVERT: D 36 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8090 (mtpp) REVERT: F 122 MET cc_start: 0.4110 (mtt) cc_final: 0.3864 (mtt) REVERT: G 41 LYS cc_start: 0.9047 (tttp) cc_final: 0.8796 (tttt) REVERT: G 115 MET cc_start: 0.8706 (mtp) cc_final: 0.8486 (mtm) REVERT: W 45 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8051 (tm-30) REVERT: W 123 MET cc_start: 0.6633 (ttp) cc_final: 0.6289 (ttt) REVERT: W 174 ARG cc_start: 0.8433 (mtm180) cc_final: 0.7931 (ttp-110) REVERT: W 178 GLN cc_start: 0.8350 (mt0) cc_final: 0.7920 (mt0) REVERT: W 212 GLN cc_start: 0.8805 (mt0) cc_final: 0.8536 (mp10) REVERT: X 208 LYS cc_start: 0.8820 (tptp) cc_final: 0.8416 (tptt) REVERT: X 262 MET cc_start: 0.8501 (mtt) cc_final: 0.8266 (mtm) outliers start: 82 outliers final: 63 residues processed: 653 average time/residue: 0.2215 time to fit residues: 234.7306 Evaluate side-chains 681 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 607 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 253 THR Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 647 ARG Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 1 residue 421 ILE Chi-restraints excluded: chain 1 residue 437 LEU Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 227 MET Chi-restraints excluded: chain 2 residue 249 MET Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 272 THR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 2 residue 445 GLN Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 104 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 335 PHE Chi-restraints excluded: chain 6 residue 348 PHE Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 378 ARG Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 158 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 206 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 384 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 371 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 60 GLN 1 87 HIS 2 22 GLN 2 223 HIS ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.188459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130347 restraints weight = 43220.192| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.68 r_work: 0.3114 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35866 Z= 0.134 Angle : 0.564 12.227 48474 Z= 0.281 Chirality : 0.040 0.202 5503 Planarity : 0.004 0.085 6101 Dihedral : 8.045 116.914 4888 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 16.07 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.38 (0.13), residues: 4226 helix: 2.06 (0.12), residues: 2011 sheet: -0.08 (0.23), residues: 507 loop : -0.09 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 193 TYR 0.019 0.001 TYR 4 79 PHE 0.030 0.001 PHE 2 269 TRP 0.015 0.001 TRP X 214 HIS 0.004 0.001 HIS 2 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (35817) covalent geometry : angle 0.54898 / 0.28 (48405) hydrogen bonds : bond 0.03576 / 2.38 ( 1679) hydrogen bonds : angle 4.07801 / 2.91 ( 4788) metal coordination : bond 0.00696 / 0.44 ( 48) metal coordination : angle 3.46208 / 2.05 ( 69) Misc. bond : bond 0.00046 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 620 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 LYS cc_start: 0.7962 (mttt) cc_final: 0.7388 (mmtp) REVERT: 0 78 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7249 (mm-30) REVERT: 0 102 ASP cc_start: 0.7926 (p0) cc_final: 0.7625 (p0) REVERT: 0 131 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6314 (mm-30) REVERT: 0 183 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7191 (mtmm) REVERT: 0 255 ASP cc_start: 0.7804 (t0) cc_final: 0.7226 (t0) REVERT: 0 259 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7626 (mtt-85) REVERT: 0 291 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7970 (mm110) REVERT: 0 397 THR cc_start: 0.8577 (t) cc_final: 0.8269 (m) REVERT: 0 528 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7458 (mm-30) REVERT: 0 620 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8630 (p) REVERT: 0 643 ARG cc_start: 0.7751 (tmm-80) cc_final: 0.7451 (ttp80) REVERT: 0 684 ARG cc_start: 0.8580 (ttp-170) cc_final: 0.8264 (ttp80) REVERT: 1 11 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8532 (mmmt) REVERT: 1 57 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7526 (pttp) REVERT: 1 252 SER cc_start: 0.8454 (m) cc_final: 0.8226 (t) REVERT: 1 262 ASN cc_start: 0.7449 (m110) cc_final: 0.7166 (m110) REVERT: 1 282 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7165 (tm-30) REVERT: 1 302 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6303 (tmm) REVERT: 1 326 ASP cc_start: 0.7099 (m-30) cc_final: 0.6701 (t70) REVERT: 1 338 ASP cc_start: 0.8336 (t0) cc_final: 0.7850 (t70) REVERT: 1 363 ASP cc_start: 0.8226 (t0) cc_final: 0.7903 (t0) REVERT: 1 421 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.6759 (pt) REVERT: 1 501 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8114 (tttp) REVERT: 1 548 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7490 (tm-30) REVERT: 1 581 LYS cc_start: 0.8153 (mttm) cc_final: 0.7600 (ttmt) REVERT: 2 85 HIS cc_start: 0.7909 (m90) cc_final: 0.7568 (m90) REVERT: 2 184 ILE cc_start: 0.8613 (mp) cc_final: 0.8333 (mt) REVERT: 2 210 MET cc_start: 0.8215 (mtp) cc_final: 0.7825 (mtm) REVERT: 2 247 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.7918 (mmt90) REVERT: 2 253 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7059 (mmm) REVERT: 2 373 MET cc_start: 0.8431 (ppp) cc_final: 0.8054 (ptt) REVERT: 2 445 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8203 (tp40) REVERT: 3 37 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8158 (ttp80) REVERT: 3 38 ILE cc_start: 0.8536 (tt) cc_final: 0.8114 (pt) REVERT: 4 207 LYS cc_start: 0.8263 (tttt) cc_final: 0.8057 (tmtt) REVERT: 4 281 ARG cc_start: 0.8350 (ptp90) cc_final: 0.7982 (ptp90) REVERT: 4 321 LYS cc_start: 0.8054 (mttt) cc_final: 0.7668 (mtpp) REVERT: 5 54 LEU cc_start: 0.8164 (mt) cc_final: 0.7895 (mm) REVERT: 6 155 ASP cc_start: 0.7905 (m-30) cc_final: 0.7638 (m-30) REVERT: 6 246 ASP cc_start: 0.8439 (p0) cc_final: 0.8056 (p0) REVERT: 6 252 ASP cc_start: 0.7716 (t0) cc_final: 0.7038 (m-30) REVERT: 6 255 VAL cc_start: 0.8752 (t) cc_final: 0.8473 (t) REVERT: 6 348 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: 6 357 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7354 (m) REVERT: 6 384 MET cc_start: 0.8108 (tpp) cc_final: 0.7071 (ptp) REVERT: 6 433 LYS cc_start: 0.8547 (mttt) cc_final: 0.7871 (mmtt) REVERT: 6 446 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6909 (tp30) REVERT: 7 121 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8521 (pp) REVERT: 7 138 ASP cc_start: 0.7709 (t0) cc_final: 0.7259 (t0) REVERT: 7 211 ASN cc_start: 0.7619 (m-40) cc_final: 0.7407 (m-40) REVERT: 7 214 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8131 (mtpp) REVERT: 7 244 MET cc_start: 0.7158 (tmm) cc_final: 0.5527 (mtm) REVERT: 7 341 TYR cc_start: 0.8267 (t80) cc_final: 0.7946 (t80) REVERT: 7 362 ILE cc_start: 0.8234 (mm) cc_final: 0.7881 (mt) REVERT: 7 367 GLU cc_start: 0.7398 (tp30) cc_final: 0.6690 (tp30) REVERT: 7 444 GLU cc_start: 0.7513 (mp0) cc_final: 0.7271 (mp0) REVERT: 7 497 MET cc_start: 0.8429 (tpp) cc_final: 0.7996 (tpp) REVERT: 7 564 GLU cc_start: 0.8392 (tp30) cc_final: 0.8021 (tp30) REVERT: 7 568 GLU cc_start: 0.8158 (tp30) cc_final: 0.7505 (tt0) REVERT: 7 578 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7377 (mtp) REVERT: 7 617 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7535 (mt-10) REVERT: 7 621 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7655 (mmtm) REVERT: 7 645 TYR cc_start: 0.7448 (m-80) cc_final: 0.6917 (m-10) REVERT: 7 666 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8213 (mm-30) REVERT: 7 729 GLN cc_start: 0.8037 (mm110) cc_final: 0.7792 (mm110) REVERT: 7 764 LEU cc_start: 0.7968 (mt) cc_final: 0.6885 (mt) REVERT: A 146 MET cc_start: 0.7875 (mmm) cc_final: 0.7611 (mmm) REVERT: A 169 ASN cc_start: 0.8605 (m-40) cc_final: 0.7795 (m110) REVERT: A 226 GLU cc_start: 0.7692 (tt0) cc_final: 0.7369 (tt0) REVERT: A 1398 MET cc_start: 0.6567 (ttt) cc_final: 0.6115 (ttm) REVERT: A 1446 ASP cc_start: 0.7610 (t0) cc_final: 0.7280 (p0) REVERT: B 1210 MET cc_start: 0.7081 (mtt) cc_final: 0.6824 (mtt) REVERT: D 31 GLN cc_start: 0.7944 (tp40) cc_final: 0.7656 (tp40) REVERT: D 36 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8095 (mtpp) REVERT: F 122 MET cc_start: 0.4117 (mtt) cc_final: 0.3865 (mtt) REVERT: G 41 LYS cc_start: 0.9044 (tttp) cc_final: 0.8788 (tttt) REVERT: W 45 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8032 (tm-30) REVERT: W 123 MET cc_start: 0.6663 (ttp) cc_final: 0.6339 (ttt) REVERT: W 174 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7938 (ttp-110) REVERT: W 178 GLN cc_start: 0.8269 (mt0) cc_final: 0.7843 (mt0) REVERT: W 212 GLN cc_start: 0.8777 (mt0) cc_final: 0.8512 (mp10) REVERT: X 208 LYS cc_start: 0.8815 (tptp) cc_final: 0.8408 (tptt) REVERT: X 262 MET cc_start: 0.8482 (mtt) cc_final: 0.8264 (mtm) outliers start: 71 outliers final: 57 residues processed: 653 average time/residue: 0.2220 time to fit residues: 235.5473 Evaluate side-chains 671 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 604 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 253 THR Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 LYS Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 1 residue 421 ILE Chi-restraints excluded: chain 1 residue 437 LEU Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 223 HIS Chi-restraints excluded: chain 2 residue 249 MET Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 272 THR Chi-restraints excluded: chain 2 residue 374 VAL Chi-restraints excluded: chain 2 residue 385 ARG Chi-restraints excluded: chain 2 residue 445 GLN Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 104 VAL Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 172 LEU Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 298 ILE Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 335 PHE Chi-restraints excluded: chain 6 residue 348 PHE Chi-restraints excluded: chain 6 residue 357 CYS Chi-restraints excluded: chain 6 residue 358 SER Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 135 SER Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 378 ARG Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 218 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 318 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 HIS ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 127 HIS ** 7 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.190713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132986 restraints weight = 43023.661| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.70 r_work: 0.3083 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 35866 Z= 0.227 Angle : 0.719 59.200 48474 Z= 0.422 Chirality : 0.041 0.319 5503 Planarity : 0.004 0.191 6101 Dihedral : 8.059 116.890 4888 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 15.97 % Favored : 82.22 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.31 % 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: 1.35 (0.13), residues: 4226 helix: 2.03 (0.12), residues: 2011 sheet: -0.08 (0.23), residues: 507 loop : -0.10 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 410 TYR 0.034 0.001 TYR 2 13 PHE 0.028 0.001 PHE 2 269 TRP 0.021 0.002 TRP 4 37 HIS 0.297 0.002 HIS 2 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (35817) covalent geometry : angle 0.70717 / 0.42 (48405) hydrogen bonds : bond 0.03672 / 2.44 ( 1679) hydrogen bonds : angle 4.09153 / 2.92 ( 4788) metal coordination : bond 0.00701 / 0.42 ( 48) metal coordination : angle 3.46690 / 2.05 ( 69) Misc. bond : bond 0.00058 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11165.99 seconds wall clock time: 191 minutes 33.01 seconds (11493.01 seconds total)