Starting phenix.real_space_refine on Sun Apr 14 15:59:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uha_42267/04_2024/8uha_42267_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uha_42267/04_2024/8uha_42267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uha_42267/04_2024/8uha_42267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uha_42267/04_2024/8uha_42267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uha_42267/04_2024/8uha_42267_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uha_42267/04_2024/8uha_42267_neut.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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: 8 Type Number sf(0) Gaussians Zn 9 6.06 5 P 81 5.49 5 Mg 1 5.21 5 S 278 5.16 5 C 29861 2.51 5 N 8266 2.21 5 O 9065 1.98 5 H 47123 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 307": "OD1" <-> "OD2" Residue "V PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 43": "OD1" <-> "OD2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 94684 Number of models: 1 Model: "" Number of chains: 29 Chain: "X" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 218 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "Y" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1816 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 7617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 7617 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 16, 'TRANS': 454} Chain breaks: 7 Chain: "W" Number of atoms: 8432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8432 Classifications: {'peptide': 530} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Chain breaks: 5 Chain: "P" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 475 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "V" Number of atoms: 8911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 8911 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 26, 'TRANS': 523} Chain: "A" Number of atoms: 22591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1417, 22591 Classifications: {'peptide': 1417} Link IDs: {'PCIS': 3, 'PTRANS': 66, 'TRANS': 1347} Chain breaks: 4 Chain: "B" Number of atoms: 18193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 18193 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4041 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 15, 'TRANS': 239} Chain breaks: 1 Chain: "D" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2046 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3414 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain breaks: 2 Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "G" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2709 Classifications: {'peptide': 171} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2333 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1793 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1051 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 753 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 886 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1208 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "U" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3054 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain breaks: 1 Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 458 SG CYS Y 16 149.527 40.295 121.989 1.00140.62 S ATOM 506 SG CYS Y 19 149.177 43.359 124.681 1.00120.39 S ATOM 721 SG CYS Y 33 152.486 42.142 124.383 1.00155.01 S ATOM 28400 SG CYS A 71 111.935 56.976 74.046 1.00215.66 S ATOM 28528 SG CYS A 81 111.612 60.112 75.297 1.00217.74 S ATOM 29011 SG CYS A 111 99.873 68.429 119.910 1.00245.29 S ATOM 29062 SG CYS A 114 96.752 66.765 120.363 1.00246.57 S ATOM 29722 SG CYS A 154 97.498 69.658 122.931 1.00243.81 S ATOM 67368 SG CYS B1119 95.356 59.928 83.344 1.00238.23 S ATOM 67412 SG CYS B1122 97.613 60.759 85.862 1.00234.75 S ATOM 67637 SG CYS B1137 98.099 57.301 82.564 1.00234.49 S ATOM 69634 SG CYS C 88 131.688 90.881 18.028 1.00182.10 S ATOM 69659 SG CYS C 90 133.601 88.532 21.729 1.00199.36 S ATOM 69719 SG CYS C 94 135.341 90.344 18.656 1.00182.43 S ATOM 84158 SG CYS I 17 139.353 118.628 139.470 1.00210.49 S ATOM 84201 SG CYS I 20 139.813 115.281 137.769 1.00220.54 S ATOM 85245 SG CYS I 86 141.067 150.687 107.992 1.00188.20 S ATOM 85294 SG CYS I 89 145.006 151.648 106.895 1.00193.14 S ATOM 85687 SG CYS I 114 143.097 148.454 105.564 1.00190.26 S ATOM 85753 SG CYS I 119 144.269 148.805 109.291 1.00184.06 S ATOM 85977 SG CYS J 7 136.218 116.960 41.425 1.00158.45 S ATOM 86547 SG CYS J 44 135.031 120.401 40.309 1.00172.21 S ATOM 86557 SG CYS J 45 138.291 119.422 38.905 1.00175.45 S ATOM 88854 SG CYS L 19 161.870 84.149 56.599 1.00284.28 S ATOM 88886 SG CYS L 22 165.012 85.020 55.380 1.00284.94 S ATOM 89116 SG CYS L 36 164.140 81.804 56.149 1.00289.13 S Time building chain proxies: 33.35, per 1000 atoms: 0.35 Number of scatterers: 94684 At special positions: 0 Unit cell: (184.95, 205.5, 161.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 9 29.99 S 278 16.00 P 81 15.00 Mg 1 11.99 O 9065 8.00 N 8266 7.00 C 29861 6.00 H 47123 1.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 60.96 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 6 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10856 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 59 sheets defined 46.9% alpha, 15.8% beta 28 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 35.42 Creating SS restraints... Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 76 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 203 removed outlier: 3.507A pdb=" N THR Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 231 through 240 removed outlier: 3.553A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 3.596A pdb=" N LEU Z 245 " --> pdb=" O VAL Z 242 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.702A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 removed outlier: 3.628A pdb=" N ILE Z 345 " --> pdb=" O ASP Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 377 through 381 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 514 through 518 Processing helix chain 'Z' and resid 631 through 633 No H-bonds generated for 'chain 'Z' and resid 631 through 633' Processing helix chain 'W' and resid 39 through 53 removed outlier: 3.631A pdb=" N THR W 53 " --> pdb=" O HIS W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 60 Proline residue: W 60 - end of helix Processing helix chain 'W' and resid 61 through 72 removed outlier: 3.942A pdb=" N ALA W 72 " --> pdb=" O ARG W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 85 removed outlier: 3.665A pdb=" N GLN W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 104 Processing helix chain 'W' and resid 107 through 127 removed outlier: 4.173A pdb=" N VAL W 111 " --> pdb=" O GLU W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 139 removed outlier: 3.962A pdb=" N GLU W 139 " --> pdb=" O ILE W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 152 removed outlier: 3.539A pdb=" N HIS W 152 " --> pdb=" O GLN W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 166 removed outlier: 3.690A pdb=" N ARG W 156 " --> pdb=" O HIS W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 169 through 182 Processing helix chain 'W' and resid 190 through 197 removed outlier: 4.468A pdb=" N GLN W 197 " --> pdb=" O THR W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 232 removed outlier: 6.241A pdb=" N GLU W 217 " --> pdb=" O LEU W 213 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU W 218 " --> pdb=" O ASP W 214 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU W 221 " --> pdb=" O GLU W 217 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS W 222 " --> pdb=" O GLU W 218 " (cutoff:3.500A) Proline residue: W 225 - end of helix removed outlier: 4.120A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 250 removed outlier: 3.633A pdb=" N GLN W 250 " --> pdb=" O SER W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 254 through 272 removed outlier: 3.990A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 284 removed outlier: 3.549A pdb=" N THR W 280 " --> pdb=" O ALA W 276 " (cutoff:3.500A) Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 303 Processing helix chain 'W' and resid 306 through 319 removed outlier: 3.589A pdb=" N VAL W 312 " --> pdb=" O ALA W 308 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 329 removed outlier: 3.706A pdb=" N ILE W 328 " --> pdb=" O PRO W 324 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 342 Processing helix chain 'W' and resid 352 through 366 Processing helix chain 'W' and resid 382 through 400 removed outlier: 4.210A pdb=" N GLU W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 404 through 409 removed outlier: 4.077A pdb=" N VAL W 408 " --> pdb=" O SER W 405 " (cutoff:3.500A) Processing helix chain 'W' and resid 410 through 419 Processing helix chain 'W' and resid 420 through 437 removed outlier: 3.517A pdb=" N GLU W 437 " --> pdb=" O TRP W 433 " (cutoff:3.500A) Processing helix chain 'W' and resid 450 through 462 Processing helix chain 'W' and resid 465 through 479 removed outlier: 3.736A pdb=" N LYS W 475 " --> pdb=" O GLN W 471 " (cutoff:3.500A) Processing helix chain 'W' and resid 485 through 506 removed outlier: 3.639A pdb=" N ARG W 506 " --> pdb=" O HIS W 502 " (cutoff:3.500A) Processing helix chain 'W' and resid 508 through 522 removed outlier: 3.856A pdb=" N VAL W 512 " --> pdb=" O TYR W 508 " (cutoff:3.500A) Processing helix chain 'W' and resid 526 through 541 removed outlier: 3.718A pdb=" N ILE W 530 " --> pdb=" O ASP W 526 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL W 540 " --> pdb=" O GLU W 536 " (cutoff:3.500A) Processing helix chain 'W' and resid 546 through 554 Processing helix chain 'W' and resid 555 through 559 removed outlier: 4.124A pdb=" N GLU W 558 " --> pdb=" O PRO W 555 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN W 559 " --> pdb=" O ILE W 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 555 through 559' Processing helix chain 'W' and resid 574 through 586 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 12 through 21 Processing helix chain 'V' and resid 25 through 37 Processing helix chain 'V' and resid 41 through 54 removed outlier: 3.966A pdb=" N GLN V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER V 46 " --> pdb=" O PRO V 42 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA V 47 " --> pdb=" O SER V 43 " (cutoff:3.500A) Proline residue: V 49 - end of helix removed outlier: 4.383A pdb=" N HIS V 54 " --> pdb=" O PHE V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 81 removed outlier: 4.460A pdb=" N PHE V 61 " --> pdb=" O PRO V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 101 Processing helix chain 'V' and resid 109 through 119 removed outlier: 3.556A pdb=" N VAL V 113 " --> pdb=" O LEU V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 134 removed outlier: 3.551A pdb=" N LEU V 128 " --> pdb=" O PRO V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 140 Processing helix chain 'V' and resid 142 through 153 removed outlier: 3.659A pdb=" N LYS V 146 " --> pdb=" O ALA V 142 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN V 148 " --> pdb=" O GLU V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 177 removed outlier: 3.615A pdb=" N PHE V 157 " --> pdb=" O ASN V 153 " (cutoff:3.500A) Proline residue: V 163 - end of helix Processing helix chain 'V' and resid 191 through 197 Processing helix chain 'V' and resid 198 through 209 Processing helix chain 'V' and resid 211 through 230 Processing helix chain 'V' and resid 232 through 249 removed outlier: 3.505A pdb=" N THR V 236 " --> pdb=" O VAL V 232 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 255 Processing helix chain 'V' and resid 258 through 273 removed outlier: 4.102A pdb=" N PHE V 262 " --> pdb=" O PRO V 258 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS V 265 " --> pdb=" O LYS V 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU V 272 " --> pdb=" O ALA V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 276 through 289 Processing helix chain 'V' and resid 295 through 306 removed outlier: 3.839A pdb=" N GLY V 299 " --> pdb=" O GLU V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 removed outlier: 3.779A pdb=" N VAL V 326 " --> pdb=" O LEU V 322 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY V 327 " --> pdb=" O GLN V 323 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN V 328 " --> pdb=" O GLU V 324 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 334 Processing helix chain 'V' and resid 335 through 350 Processing helix chain 'V' and resid 350 through 357 Processing helix chain 'V' and resid 366 through 372 removed outlier: 3.513A pdb=" N ILE V 370 " --> pdb=" O GLU V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 372 through 393 Processing helix chain 'V' and resid 408 through 416 removed outlier: 3.922A pdb=" N THR V 412 " --> pdb=" O PRO V 408 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 436 Processing helix chain 'V' and resid 437 through 445 Processing helix chain 'V' and resid 451 through 457 removed outlier: 3.611A pdb=" N ASP V 454 " --> pdb=" O THR V 451 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ALA V 456 " --> pdb=" O GLY V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 458 through 469 Processing helix chain 'V' and resid 473 through 477 removed outlier: 3.923A pdb=" N PHE V 476 " --> pdb=" O ALA V 473 " (cutoff:3.500A) Processing helix chain 'V' and resid 478 through 486 Processing helix chain 'V' and resid 489 through 493 removed outlier: 3.612A pdb=" N ALA V 493 " --> pdb=" O PHE V 490 " (cutoff:3.500A) Processing helix chain 'V' and resid 497 through 512 Processing helix chain 'V' and resid 516 through 527 Processing helix chain 'V' and resid 534 through 553 removed outlier: 3.779A pdb=" N LYS V 538 " --> pdb=" O GLY V 534 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP V 552 " --> pdb=" O LEU V 548 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS V 553 " --> pdb=" O GLU V 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.608A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.622A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.541A pdb=" N ALA A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.530A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.802A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.814A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.867A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.550A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 removed outlier: 4.153A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.978A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.596A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.236A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.541A pdb=" N MET A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.786A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1186 through 1197 removed outlier: 4.443A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.617A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.680A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.946A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 removed outlier: 3.951A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.737A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.541A pdb=" N VAL A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1441 " --> pdb=" O ASP A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'A' and resid 1466 through 1470 removed outlier: 4.049A pdb=" N CYS A1470 " --> pdb=" O GLY A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1482 Processing helix chain 'B' and resid 18 through 38 removed outlier: 3.896A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 245 through 253 removed outlier: 4.118A pdb=" N LYS B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.661A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.817A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.805A pdb=" N ALA B 560 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.529A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.538A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.720A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.725A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.520A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.954A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 4.442A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.847A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.675A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.525A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.990A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.563A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.727A pdb=" N PHE E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 5.789A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.255A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.877A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.732A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.189A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'U' and resid 10 through 18 Processing helix chain 'U' and resid 28 through 33 Processing helix chain 'U' and resid 34 through 42 removed outlier: 4.258A pdb=" N ARG U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 59 Processing helix chain 'U' and resid 60 through 63 Processing helix chain 'U' and resid 64 through 71 removed outlier: 3.833A pdb=" N MET U 71 " --> pdb=" O THR U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 84 Processing helix chain 'U' and resid 87 through 98 Processing helix chain 'U' and resid 99 through 104 removed outlier: 3.988A pdb=" N THR U 103 " --> pdb=" O SER U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 131 Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 145 through 154 Processing helix chain 'U' and resid 170 through 188 Processing helix chain 'U' and resid 258 through 262 Processing sheet with id=AA1, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'Y' and resid 56 through 63 removed outlier: 4.536A pdb=" N SER Y 56 " --> pdb=" O THR Y 90 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE Y 60 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA Y 86 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA Y 62 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL Y 84 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 214 through 216 removed outlier: 3.839A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 278 through 280 removed outlier: 5.759A pdb=" N VAL Z 293 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS Z 306 " --> pdb=" O VAL Z 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR Z 295 " --> pdb=" O SER Z 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id=AA6, first strand: chain 'Z' and resid 453 through 454 removed outlier: 3.637A pdb=" N ARG Z 469 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Z' and resid 477 through 479 removed outlier: 7.210A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Z' and resid 539 through 543 removed outlier: 6.755A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AB1, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.627A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 742 through 746 removed outlier: 7.103A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 367 through 370 removed outlier: 6.551A pdb=" N VAL W 367 " --> pdb=" O ILE W 378 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE W 378 " --> pdb=" O VAL W 367 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR W 369 " --> pdb=" O VAL W 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.585A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AB6, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.497A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.443A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 264 through 265 removed outlier: 3.827A pdb=" N VAL A 264 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.679A pdb=" N VAL A 359 " --> pdb=" O LEU B1084 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 377 through 380 removed outlier: 7.764A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 377 through 380 removed outlier: 3.757A pdb=" N HIS B1060 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.146A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.768A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AC6, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.474A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.952A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'A' and resid 872 through 874 removed outlier: 6.674A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AD2, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.146A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.623A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.749A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A1173 " --> pdb=" O ASN I 56 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN I 56 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AD6, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AD7, first strand: chain 'B' and resid 140 through 153 removed outlier: 4.386A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N LYS U 255 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 91 " --> pdb=" O LYS U 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD9, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AE1, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.988A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 531 through 534 removed outlier: 4.449A pdb=" N ARG B 620 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AE4, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.704A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.875A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 926 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR B 901 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.875A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 926 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR B 901 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 759 through 760 removed outlier: 3.906A pdb=" N THR B 760 " --> pdb=" O GLY B 997 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.052A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 828 through 829 Processing sheet with id=AF1, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.795A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.615A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.635A pdb=" N GLN C 157 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.688A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.353A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.888A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AF8, first strand: chain 'G' and resid 2 through 13 removed outlier: 11.539A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AG1, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.686A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AG3, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AG4, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AG5, first strand: chain 'K' and resid 19 through 23 2166 hydrogen bonds defined for protein. 6066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 40.57 Time building geometry restraints manager: 64.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 47018 1.03 - 1.23: 133 1.23 - 1.42: 19851 1.42 - 1.62: 28287 1.62 - 1.82: 440 Bond restraints: 95729 Sorted by residual: bond pdb=" C PHE B 713 " pdb=" O PHE B 713 " ideal model delta sigma weight residual 1.233 1.265 -0.032 4.80e-03 4.34e+04 4.52e+01 bond pdb=" CA PRO U 26 " pdb=" C PRO U 26 " ideal model delta sigma weight residual 1.517 1.545 -0.027 9.30e-03 1.16e+04 8.70e+00 bond pdb=" CD LYS X 23 " pdb=" HD2 LYS X 23 " ideal model delta sigma weight residual 0.970 0.915 0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C LEU G 13 " pdb=" N HIS G 14 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.83e-02 1.25e+03 6.27e+00 bond pdb=" CA LEU Z 736 " pdb=" C LEU Z 736 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.31e-02 5.83e+03 5.93e+00 ... (remaining 95724 not shown) Histogram of bond angle deviations from ideal: 96.45 - 104.04: 1016 104.04 - 111.63: 107515 111.63 - 119.21: 27262 119.21 - 126.80: 36928 126.80 - 134.39: 798 Bond angle restraints: 173519 Sorted by residual: angle pdb=" C GLY W 345 " pdb=" N ALA W 346 " pdb=" CA ALA W 346 " ideal model delta sigma weight residual 121.70 130.63 -8.93 1.80e+00 3.09e-01 2.46e+01 angle pdb=" N GLY Z 490 " pdb=" CA GLY Z 490 " pdb=" C GLY Z 490 " ideal model delta sigma weight residual 110.29 116.09 -5.80 1.28e+00 6.10e-01 2.06e+01 angle pdb=" N GLN X 16 " pdb=" CA GLN X 16 " pdb=" C GLN X 16 " ideal model delta sigma weight residual 111.11 116.50 -5.39 1.20e+00 6.94e-01 2.02e+01 angle pdb=" C3' U P 6 " pdb=" O3' U P 6 " pdb=" P G P 7 " ideal model delta sigma weight residual 120.20 126.92 -6.72 1.50e+00 4.44e-01 2.01e+01 angle pdb=" CB LYS X 24 " pdb=" CG LYS X 24 " pdb=" CD LYS X 24 " ideal model delta sigma weight residual 111.30 120.81 -9.51 2.30e+00 1.89e-01 1.71e+01 ... (remaining 173514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 42771 32.87 - 65.74: 1642 65.74 - 98.61: 78 98.61 - 131.48: 0 131.48 - 164.35: 4 Dihedral angle restraints: 44495 sinusoidal: 25247 harmonic: 19248 Sorted by residual: dihedral pdb=" O4' C P 17 " pdb=" C1' C P 17 " pdb=" N1 C P 17 " pdb=" C2 C P 17 " ideal model delta sinusoidal sigma weight residual 232.00 67.65 164.35 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" CA LYS X 21 " pdb=" C LYS X 21 " pdb=" N LEU X 22 " pdb=" CA LEU X 22 " ideal model delta harmonic sigma weight residual 180.00 147.80 32.20 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" O4' U P 3 " pdb=" C1' U P 3 " pdb=" N1 U P 3 " pdb=" C2 U P 3 " ideal model delta sinusoidal sigma weight residual -160.00 -73.85 -86.15 1 1.50e+01 4.44e-03 3.98e+01 ... (remaining 44492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 5206 0.042 - 0.085: 1659 0.085 - 0.127: 468 0.127 - 0.169: 120 0.169 - 0.212: 6 Chirality restraints: 7459 Sorted by residual: chirality pdb=" CA ILE Z 721 " pdb=" N ILE Z 721 " pdb=" C ILE Z 721 " pdb=" CB ILE Z 721 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C3' U P 6 " pdb=" C4' U P 6 " pdb=" O3' U P 6 " pdb=" C2' U P 6 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ASN I 41 " pdb=" N ASN I 41 " pdb=" C ASN I 41 " pdb=" CB ASN I 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 7456 not shown) Planarity restraints: 13737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 733 " 0.083 9.50e-02 1.11e+02 3.97e-02 1.52e+01 pdb=" NE ARG Z 733 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG Z 733 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 733 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 733 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG Z 733 " -0.040 2.00e-02 2.50e+03 pdb="HH12 ARG Z 733 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG Z 733 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 719 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO B 720 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 720 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 720 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER V 494 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO V 495 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO V 495 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO V 495 " -0.039 5.00e-02 4.00e+02 ... (remaining 13734 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.93: 456 1.93 - 2.60: 102763 2.60 - 3.26: 298098 3.26 - 3.93: 374827 3.93 - 4.60: 585059 Nonbonded interactions: 1361203 Sorted by model distance: nonbonded pdb=" H CYS I 20 " pdb="ZN ZN I 201 " model vdw 1.260 1.760 nonbonded pdb="HO3' C P 17 " pdb="MG MG P 101 " model vdw 1.323 1.700 nonbonded pdb=" HB3 CYS L 39 " pdb="ZN ZN L 101 " model vdw 1.549 1.930 nonbonded pdb=" O3' C P 17 " pdb="MG MG P 101 " model vdw 1.567 2.050 nonbonded pdb=" N CYS J 45 " pdb="ZN ZN J 101 " model vdw 1.658 2.260 ... (remaining 1361198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.690 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: 0.000 Extract box with map and model: 32.940 Check model and map are aligned: 1.110 Set scattering table: 0.710 Process input model: 295.020 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 351.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 48606 Z= 0.353 Angle : 0.833 10.634 66004 Z= 0.446 Chirality : 0.046 0.212 7459 Planarity : 0.006 0.071 8233 Dihedral : 15.351 164.347 18775 Min Nonbonded Distance : 1.567 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.77 % Allowed : 4.58 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.11), residues: 5669 helix: 0.04 (0.10), residues: 2300 sheet: -1.53 (0.17), residues: 696 loop : -1.08 (0.12), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Y 70 HIS 0.010 0.001 HIS K 69 PHE 0.038 0.002 PHE B 320 TYR 0.018 0.002 TYR B 388 ARG 0.043 0.001 ARG B 859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 518 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 479 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 17 LYS cc_start: 0.6406 (mttt) cc_final: 0.6014 (mttm) REVERT: X 21 LYS cc_start: 0.5323 (OUTLIER) cc_final: 0.4895 (tmtt) REVERT: X 23 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7745 (tptt) REVERT: Z 738 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7323 (t) REVERT: W 100 TRP cc_start: 0.1798 (m100) cc_final: 0.1506 (m100) REVERT: W 149 MET cc_start: 0.6705 (mmp) cc_final: 0.6454 (mmt) REVERT: W 171 MET cc_start: 0.7939 (ttt) cc_final: 0.7711 (ttt) REVERT: W 362 TYR cc_start: 0.6369 (t80) cc_final: 0.6168 (t80) REVERT: A 42 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8188 (ptpt) REVERT: A 309 LEU cc_start: 0.9360 (tp) cc_final: 0.9125 (tp) REVERT: A 750 ASP cc_start: 0.9343 (m-30) cc_final: 0.9129 (m-30) REVERT: A 811 ILE cc_start: 0.9798 (OUTLIER) cc_final: 0.9501 (mt) REVERT: A 868 MET cc_start: 0.8868 (ttm) cc_final: 0.8605 (ttm) REVERT: A 961 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8890 (tm-30) REVERT: A 1132 LYS cc_start: 0.8053 (mppt) cc_final: 0.7834 (mptt) REVERT: A 1344 MET cc_start: 0.8428 (tpt) cc_final: 0.8198 (tpt) REVERT: A 1412 MET cc_start: 0.8757 (ttp) cc_final: 0.8417 (tmm) REVERT: B 108 MET cc_start: 0.8613 (ttp) cc_final: 0.8394 (ptm) REVERT: B 368 MET cc_start: 0.9550 (mtp) cc_final: 0.9302 (ttt) REVERT: B 508 MET cc_start: 0.8805 (mmt) cc_final: 0.8479 (mmm) REVERT: B 516 GLU cc_start: 0.8736 (tp30) cc_final: 0.8525 (tp30) REVERT: B 550 MET cc_start: 0.9154 (tmm) cc_final: 0.8758 (tmm) REVERT: B 870 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8106 (t) REVERT: B 908 MET cc_start: 0.8701 (ppp) cc_final: 0.8233 (tmm) REVERT: B 1089 MET cc_start: 0.8343 (mmm) cc_final: 0.8140 (mmm) REVERT: B 1092 ASP cc_start: 0.8995 (m-30) cc_final: 0.8783 (m-30) REVERT: B 1155 CYS cc_start: 0.9468 (t) cc_final: 0.9203 (t) REVERT: D 24 LYS cc_start: 0.9131 (pttp) cc_final: 0.8872 (mppt) REVERT: E 103 LEU cc_start: 0.9685 (tp) cc_final: 0.9447 (tt) REVERT: E 167 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8720 (mt-10) REVERT: F 109 TYR cc_start: 0.8370 (m-80) cc_final: 0.8099 (m-10) REVERT: G 1 MET cc_start: 0.8473 (tpp) cc_final: 0.8240 (tpp) REVERT: H 123 MET cc_start: 0.9125 (ttp) cc_final: 0.8707 (ttp) REVERT: I 78 LEU cc_start: 0.9440 (mt) cc_final: 0.8992 (mt) REVERT: J 48 MET cc_start: 0.9179 (mmm) cc_final: 0.8958 (mmm) REVERT: L 44 MET cc_start: 0.7666 (mmt) cc_final: 0.7310 (mmt) outliers start: 39 outliers final: 8 residues processed: 515 average time/residue: 1.3857 time to fit residues: 1133.1473 Evaluate side-chains 367 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 353 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Z residue 738 SER Chi-restraints excluded: chain W residue 139 GLU Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1142 ASN Chi-restraints excluded: chain U residue 181 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 4.9990 chunk 434 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 449 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 520 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN W 278 GLN W 379 ASN V 321 HIS V 391 GLN V 435 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN K 49 GLN U 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 48606 Z= 0.337 Angle : 0.618 7.057 66004 Z= 0.341 Chirality : 0.040 0.160 7459 Planarity : 0.005 0.093 8233 Dihedral : 13.504 162.809 7223 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.90 % Allowed : 8.21 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.11), residues: 5669 helix: 0.35 (0.10), residues: 2353 sheet: -1.48 (0.18), residues: 676 loop : -1.03 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 12 HIS 0.007 0.001 HIS A 84 PHE 0.018 0.001 PHE B 320 TYR 0.013 0.001 TYR B 33 ARG 0.014 0.001 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 347 time to evaluate : 5.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7732 (tptt) REVERT: W 100 TRP cc_start: 0.1877 (m100) cc_final: 0.1594 (m100) REVERT: W 149 MET cc_start: 0.6864 (mmp) cc_final: 0.6654 (mmt) REVERT: A 266 MET cc_start: 0.1678 (ptm) cc_final: 0.1195 (ptt) REVERT: A 309 LEU cc_start: 0.9381 (tp) cc_final: 0.9174 (tp) REVERT: A 868 MET cc_start: 0.8931 (ttm) cc_final: 0.8657 (ttm) REVERT: A 961 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 1228 MET cc_start: 0.8833 (ttm) cc_final: 0.8620 (mtp) REVERT: A 1344 MET cc_start: 0.8534 (tpt) cc_final: 0.8309 (tpp) REVERT: B 508 MET cc_start: 0.8876 (mmt) cc_final: 0.8491 (mmm) REVERT: B 550 MET cc_start: 0.9202 (tmm) cc_final: 0.8695 (tmm) REVERT: B 603 MET cc_start: 0.8373 (ptp) cc_final: 0.8114 (ptp) REVERT: B 791 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8660 (mm-30) REVERT: B 1089 MET cc_start: 0.8489 (mmm) cc_final: 0.8259 (mmm) REVERT: B 1092 ASP cc_start: 0.9032 (m-30) cc_final: 0.8815 (m-30) REVERT: B 1151 MET cc_start: 0.9507 (ptm) cc_final: 0.8560 (ptp) REVERT: B 1155 CYS cc_start: 0.9438 (t) cc_final: 0.8871 (t) REVERT: B 1172 MET cc_start: 0.8452 (mmm) cc_final: 0.8068 (mmm) REVERT: H 123 MET cc_start: 0.9297 (ttp) cc_final: 0.8496 (tmm) REVERT: U 264 MET cc_start: 0.5074 (mmt) cc_final: 0.4672 (mmm) outliers start: 46 outliers final: 26 residues processed: 380 average time/residue: 1.3202 time to fit residues: 795.2497 Evaluate side-chains 351 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 324 time to evaluate : 6.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 208 SER Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 465 LEU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1142 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 80 GLN Chi-restraints excluded: chain U residue 181 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 433 optimal weight: 4.9990 chunk 354 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 521 optimal weight: 6.9990 chunk 563 optimal weight: 9.9990 chunk 464 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 418 optimal weight: 0.0060 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 418 HIS ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 48606 Z= 0.329 Angle : 0.613 10.574 66004 Z= 0.335 Chirality : 0.040 0.217 7459 Planarity : 0.004 0.057 8233 Dihedral : 13.365 168.193 7205 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.32 % Allowed : 9.57 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.11), residues: 5669 helix: 0.38 (0.10), residues: 2355 sheet: -1.48 (0.18), residues: 720 loop : -1.16 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.015 0.001 HIS V 512 PHE 0.017 0.001 PHE B 544 TYR 0.019 0.002 TYR H 48 ARG 0.009 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 396 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 329 time to evaluate : 6.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7795 (tptt) REVERT: W 100 TRP cc_start: 0.1924 (m100) cc_final: 0.1650 (m100) REVERT: W 149 MET cc_start: 0.7161 (mmp) cc_final: 0.6889 (mmt) REVERT: A 309 LEU cc_start: 0.9339 (tp) cc_final: 0.9138 (tp) REVERT: A 565 MET cc_start: 0.8865 (mmm) cc_final: 0.8458 (mmm) REVERT: A 868 MET cc_start: 0.8919 (ttm) cc_final: 0.8496 (ttm) REVERT: A 961 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8739 (tm-30) REVERT: A 1228 MET cc_start: 0.8772 (ttm) cc_final: 0.8426 (mtp) REVERT: B 508 MET cc_start: 0.8932 (mmt) cc_final: 0.8657 (mmm) REVERT: B 550 MET cc_start: 0.9158 (tmm) cc_final: 0.8762 (tmm) REVERT: B 603 MET cc_start: 0.8472 (ptp) cc_final: 0.8242 (ptp) REVERT: B 791 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8529 (mm-30) REVERT: B 1089 MET cc_start: 0.8511 (mmm) cc_final: 0.8224 (mmp) REVERT: B 1151 MET cc_start: 0.9403 (ptm) cc_final: 0.8467 (ptp) REVERT: B 1155 CYS cc_start: 0.9480 (t) cc_final: 0.8926 (t) REVERT: B 1171 MET cc_start: 0.9043 (ptp) cc_final: 0.8771 (ptp) REVERT: B 1172 MET cc_start: 0.8277 (mmm) cc_final: 0.7955 (mmm) REVERT: G 131 MET cc_start: 0.5334 (ptp) cc_final: 0.4928 (pmm) REVERT: H 37 MET cc_start: 0.8720 (mmm) cc_final: 0.8417 (mmm) REVERT: H 123 MET cc_start: 0.9316 (ttp) cc_final: 0.8498 (tmm) REVERT: U 264 MET cc_start: 0.5122 (mmt) cc_final: 0.4740 (mmm) outliers start: 67 outliers final: 49 residues processed: 379 average time/residue: 1.2857 time to fit residues: 784.6852 Evaluate side-chains 360 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 310 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 430 GLU Chi-restraints excluded: chain W residue 58 MET Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain W residue 560 ASP Chi-restraints excluded: chain V residue 95 ASP Chi-restraints excluded: chain V residue 235 CYS Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 245 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1142 ASN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 181 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 515 optimal weight: 10.0000 chunk 391 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 350 optimal weight: 8.9990 chunk 523 optimal weight: 0.7980 chunk 553 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 495 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS K 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48606 Z= 0.203 Angle : 0.528 6.916 66004 Z= 0.287 Chirality : 0.039 0.159 7459 Planarity : 0.004 0.054 8233 Dihedral : 13.258 171.937 7198 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.08 % Allowed : 10.41 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5669 helix: 0.72 (0.11), residues: 2353 sheet: -1.37 (0.18), residues: 713 loop : -1.02 (0.13), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.007 0.001 HIS V 512 PHE 0.017 0.001 PHE B 320 TYR 0.013 0.001 TYR W 69 ARG 0.007 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 324 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7677 (tptt) REVERT: W 100 TRP cc_start: 0.1797 (m100) cc_final: 0.1507 (m100) REVERT: A 34 MET cc_start: 0.9013 (tmm) cc_final: 0.8705 (ppp) REVERT: A 524 MET cc_start: 0.8506 (mmm) cc_final: 0.8295 (mmm) REVERT: A 673 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8910 (mm-40) REVERT: A 868 MET cc_start: 0.8900 (ttm) cc_final: 0.8563 (ttm) REVERT: A 961 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8746 (tm-30) REVERT: A 1412 MET cc_start: 0.8117 (tmm) cc_final: 0.7904 (tmm) REVERT: B 508 MET cc_start: 0.8891 (mmt) cc_final: 0.8620 (mmm) REVERT: B 550 MET cc_start: 0.9144 (tmm) cc_final: 0.8818 (tmm) REVERT: B 603 MET cc_start: 0.8420 (ptp) cc_final: 0.8210 (ptp) REVERT: B 791 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8565 (mm-30) REVERT: B 1048 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: B 1089 MET cc_start: 0.8465 (mmm) cc_final: 0.8187 (mmp) REVERT: B 1163 MET cc_start: 0.9415 (mtp) cc_final: 0.9207 (mtp) REVERT: B 1171 MET cc_start: 0.8975 (ptp) cc_final: 0.8684 (ptp) REVERT: B 1172 MET cc_start: 0.8190 (mmm) cc_final: 0.7866 (mmm) REVERT: G 131 MET cc_start: 0.5306 (ptp) cc_final: 0.4891 (pmm) REVERT: H 123 MET cc_start: 0.9258 (ttp) cc_final: 0.8541 (tmm) REVERT: H 145 MET cc_start: 0.6753 (tmm) cc_final: 0.6525 (tmm) REVERT: I 75 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8209 (t0) REVERT: I 78 LEU cc_start: 0.9336 (mt) cc_final: 0.9057 (mt) REVERT: U 264 MET cc_start: 0.5053 (mmt) cc_final: 0.4664 (mmm) outliers start: 55 outliers final: 39 residues processed: 362 average time/residue: 1.3295 time to fit residues: 772.6429 Evaluate side-chains 343 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 301 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1142 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 181 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 461 optimal weight: 8.9990 chunk 314 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 412 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 472 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 497 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 ASN D 38 HIS K 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 48606 Z= 0.351 Angle : 0.602 7.048 66004 Z= 0.329 Chirality : 0.040 0.156 7459 Planarity : 0.004 0.053 8233 Dihedral : 13.283 179.482 7197 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.87 % Allowed : 11.12 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.11), residues: 5669 helix: 0.52 (0.10), residues: 2358 sheet: -1.45 (0.18), residues: 734 loop : -1.22 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.006 0.001 HIS A 995 PHE 0.016 0.001 PHE B 544 TYR 0.017 0.002 TYR V 403 ARG 0.006 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 299 time to evaluate : 6.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7816 (tptt) REVERT: A 34 MET cc_start: 0.9007 (tmm) cc_final: 0.8696 (ppp) REVERT: A 673 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8786 (mm-40) REVERT: A 677 ASN cc_start: 0.9275 (m-40) cc_final: 0.9017 (m-40) REVERT: A 868 MET cc_start: 0.8932 (ttm) cc_final: 0.8663 (ttm) REVERT: A 961 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8758 (tm-30) REVERT: A 1228 MET cc_start: 0.8748 (ttm) cc_final: 0.8335 (mtp) REVERT: A 1412 MET cc_start: 0.8132 (tmm) cc_final: 0.7923 (tmm) REVERT: B 215 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: B 508 MET cc_start: 0.8893 (mmt) cc_final: 0.8647 (mmm) REVERT: B 529 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8466 (mmm) REVERT: B 550 MET cc_start: 0.9175 (tmm) cc_final: 0.8849 (tmm) REVERT: B 728 MET cc_start: 0.8963 (mtm) cc_final: 0.8688 (mtm) REVERT: B 791 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 908 MET cc_start: 0.8786 (ppp) cc_final: 0.8518 (ppp) REVERT: B 1048 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8968 (m-80) REVERT: B 1089 MET cc_start: 0.8452 (mmm) cc_final: 0.8116 (mmp) REVERT: B 1171 MET cc_start: 0.8916 (ptp) cc_final: 0.8601 (ptp) REVERT: B 1172 MET cc_start: 0.8184 (mmm) cc_final: 0.7878 (mmm) REVERT: E 91 CYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8865 (p) REVERT: G 131 MET cc_start: 0.5244 (ptp) cc_final: 0.4798 (pmm) REVERT: H 123 MET cc_start: 0.9310 (ttp) cc_final: 0.8539 (tmm) REVERT: H 145 MET cc_start: 0.6945 (tmm) cc_final: 0.6645 (tmm) REVERT: U 126 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: U 264 MET cc_start: 0.5069 (mmt) cc_final: 0.4663 (mmm) outliers start: 95 outliers final: 66 residues processed: 373 average time/residue: 1.2498 time to fit residues: 757.4866 Evaluate side-chains 363 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 291 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 430 GLU Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 410 GLU Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain V residue 95 ASP Chi-restraints excluded: chain V residue 235 CYS Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 126 GLU Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain U residue 187 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 186 optimal weight: 9.9990 chunk 498 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 325 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 554 optimal weight: 5.9990 chunk 460 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 501 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 48606 Z= 0.240 Angle : 0.538 7.869 66004 Z= 0.292 Chirality : 0.039 0.157 7459 Planarity : 0.004 0.052 8233 Dihedral : 13.219 174.883 7195 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.59 % Allowed : 11.92 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 5669 helix: 0.78 (0.11), residues: 2350 sheet: -1.41 (0.18), residues: 729 loop : -1.09 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.005 0.001 HIS V 512 PHE 0.016 0.001 PHE B 320 TYR 0.012 0.001 TYR H 48 ARG 0.005 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 298 time to evaluate : 6.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7830 (tptt) REVERT: W 473 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8321 (tt) REVERT: W 500 MET cc_start: 0.8389 (tpp) cc_final: 0.8157 (mpp) REVERT: A 34 MET cc_start: 0.9062 (tmm) cc_final: 0.8762 (ppp) REVERT: A 514 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8760 (tm-30) REVERT: A 636 ILE cc_start: 0.9442 (pt) cc_final: 0.9237 (mt) REVERT: A 673 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8736 (mm-40) REVERT: A 677 ASN cc_start: 0.9233 (m-40) cc_final: 0.8971 (m-40) REVERT: A 868 MET cc_start: 0.8937 (ttm) cc_final: 0.8650 (ttm) REVERT: A 961 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 1412 MET cc_start: 0.8138 (tmm) cc_final: 0.7920 (tmm) REVERT: A 1459 MET cc_start: 0.9305 (ptp) cc_final: 0.8926 (ptp) REVERT: B 508 MET cc_start: 0.8883 (mmt) cc_final: 0.8651 (mmm) REVERT: B 529 MET cc_start: 0.8735 (mmm) cc_final: 0.8379 (mmm) REVERT: B 550 MET cc_start: 0.9132 (tmm) cc_final: 0.8799 (tmm) REVERT: B 728 MET cc_start: 0.8945 (mtm) cc_final: 0.8670 (mtm) REVERT: B 791 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8569 (mm-30) REVERT: B 1048 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.9010 (m-80) REVERT: B 1089 MET cc_start: 0.8493 (mmm) cc_final: 0.8108 (mmp) REVERT: B 1124 ILE cc_start: 0.8949 (mm) cc_final: 0.8328 (pt) REVERT: B 1171 MET cc_start: 0.8939 (ptp) cc_final: 0.8619 (ptp) REVERT: B 1172 MET cc_start: 0.8193 (mmm) cc_final: 0.7889 (mmm) REVERT: E 91 CYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8889 (p) REVERT: G 131 MET cc_start: 0.5266 (ptp) cc_final: 0.4779 (pmm) REVERT: H 123 MET cc_start: 0.9261 (ttp) cc_final: 0.8559 (tmm) REVERT: U 126 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: U 264 MET cc_start: 0.5026 (mmt) cc_final: 0.4615 (mmm) outliers start: 81 outliers final: 66 residues processed: 359 average time/residue: 1.2564 time to fit residues: 741.1386 Evaluate side-chains 360 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 289 time to evaluate : 5.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain W residue 58 MET Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 360 LEU Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 473 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain W residue 560 ASP Chi-restraints excluded: chain V residue 95 ASP Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 249 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 126 GLU Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 170 LYS Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 187 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 534 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 315 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 313 optimal weight: 0.8980 chunk 466 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 552 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 48606 Z= 0.169 Angle : 0.506 8.556 66004 Z= 0.271 Chirality : 0.039 0.163 7459 Planarity : 0.004 0.052 8233 Dihedral : 13.108 173.007 7195 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.34 % Allowed : 12.36 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5669 helix: 1.12 (0.11), residues: 2354 sheet: -1.27 (0.18), residues: 724 loop : -0.89 (0.13), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.007 0.001 HIS A 84 PHE 0.017 0.001 PHE B 320 TYR 0.011 0.001 TYR B 33 ARG 0.006 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 306 time to evaluate : 5.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7925 (tptt) REVERT: A 34 MET cc_start: 0.9065 (tmm) cc_final: 0.8762 (ppp) REVERT: A 355 MET cc_start: 0.9485 (mmm) cc_final: 0.9267 (mmm) REVERT: A 673 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8645 (mm-40) REVERT: A 677 ASN cc_start: 0.9211 (m-40) cc_final: 0.8956 (m-40) REVERT: A 868 MET cc_start: 0.8892 (ttm) cc_final: 0.8563 (ttm) REVERT: A 961 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 1412 MET cc_start: 0.8153 (tmm) cc_final: 0.7928 (tmm) REVERT: A 1459 MET cc_start: 0.9332 (ptp) cc_final: 0.8928 (ptp) REVERT: B 508 MET cc_start: 0.8841 (mmt) cc_final: 0.8625 (mmm) REVERT: B 529 MET cc_start: 0.8730 (mmm) cc_final: 0.8395 (mmm) REVERT: B 550 MET cc_start: 0.9144 (tmm) cc_final: 0.8800 (tmm) REVERT: B 728 MET cc_start: 0.8905 (mtm) cc_final: 0.8627 (mtm) REVERT: B 791 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 1048 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8936 (m-80) REVERT: B 1089 MET cc_start: 0.8471 (mmm) cc_final: 0.8100 (mmp) REVERT: B 1124 ILE cc_start: 0.8986 (mm) cc_final: 0.8353 (pt) REVERT: B 1171 MET cc_start: 0.8901 (ptp) cc_final: 0.8636 (ptp) REVERT: B 1172 MET cc_start: 0.8179 (mmm) cc_final: 0.7844 (mmm) REVERT: H 123 MET cc_start: 0.9214 (ttp) cc_final: 0.8592 (tmm) REVERT: U 126 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: U 264 MET cc_start: 0.5038 (mmt) cc_final: 0.4616 (mmm) outliers start: 68 outliers final: 54 residues processed: 358 average time/residue: 1.2387 time to fit residues: 710.8428 Evaluate side-chains 353 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 296 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 29 GLU Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 360 LEU Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 126 GLU Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 170 LYS Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 187 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 341 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 329 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 351 optimal weight: 5.9990 chunk 376 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 51 optimal weight: 50.0000 chunk 434 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 GLN ** V 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 48606 Z= 0.350 Angle : 0.594 7.342 66004 Z= 0.323 Chirality : 0.039 0.182 7459 Planarity : 0.004 0.069 8233 Dihedral : 13.150 166.562 7195 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.83 % Allowed : 12.36 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.11), residues: 5669 helix: 0.77 (0.11), residues: 2353 sheet: -1.38 (0.18), residues: 732 loop : -1.19 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 453 HIS 0.006 0.001 HIS B 741 PHE 0.021 0.001 PHE B1159 TYR 0.012 0.001 TYR B 338 ARG 0.010 0.001 ARG V 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 290 time to evaluate : 5.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8235 (mptp) cc_final: 0.7960 (tptt) REVERT: A 34 MET cc_start: 0.9122 (tmm) cc_final: 0.8836 (ppp) REVERT: A 355 MET cc_start: 0.9525 (mmm) cc_final: 0.9308 (mmm) REVERT: A 673 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8761 (mm-40) REVERT: A 677 ASN cc_start: 0.9271 (m-40) cc_final: 0.8978 (m-40) REVERT: A 868 MET cc_start: 0.8981 (ttm) cc_final: 0.8736 (ttm) REVERT: A 961 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 1228 MET cc_start: 0.8679 (ttm) cc_final: 0.8116 (mtt) REVERT: A 1412 MET cc_start: 0.8170 (tmm) cc_final: 0.7941 (tmm) REVERT: A 1459 MET cc_start: 0.9345 (ptp) cc_final: 0.8939 (ptp) REVERT: B 508 MET cc_start: 0.8842 (mmt) cc_final: 0.8635 (mmm) REVERT: B 529 MET cc_start: 0.8799 (mmm) cc_final: 0.8467 (mmm) REVERT: B 550 MET cc_start: 0.9123 (tmm) cc_final: 0.8769 (tmm) REVERT: B 728 MET cc_start: 0.8922 (mtm) cc_final: 0.8647 (mtm) REVERT: B 908 MET cc_start: 0.8806 (ppp) cc_final: 0.8532 (ppp) REVERT: B 1048 TYR cc_start: 0.9391 (OUTLIER) cc_final: 0.9002 (m-80) REVERT: B 1089 MET cc_start: 0.8547 (mmm) cc_final: 0.8047 (mmp) REVERT: B 1171 MET cc_start: 0.8935 (ptp) cc_final: 0.8650 (ptp) REVERT: B 1172 MET cc_start: 0.8166 (mmm) cc_final: 0.7889 (mmm) REVERT: F 109 TYR cc_start: 0.8565 (m-10) cc_final: 0.8164 (m-10) REVERT: H 123 MET cc_start: 0.9298 (ttp) cc_final: 0.8615 (tmm) REVERT: U 126 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: U 264 MET cc_start: 0.5124 (mmt) cc_final: 0.4913 (mmt) outliers start: 93 outliers final: 79 residues processed: 364 average time/residue: 1.2818 time to fit residues: 754.3439 Evaluate side-chains 367 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 286 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 430 GLU Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain W residue 58 MET Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 360 LEU Chi-restraints excluded: chain W residue 419 ARG Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain W residue 560 ASP Chi-restraints excluded: chain V residue 61 PHE Chi-restraints excluded: chain V residue 235 CYS Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 126 GLU Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 170 LYS Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 187 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 502 optimal weight: 3.9990 chunk 529 optimal weight: 4.9990 chunk 482 optimal weight: 9.9990 chunk 514 optimal weight: 7.9990 chunk 528 optimal weight: 0.6980 chunk 309 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 404 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 465 optimal weight: 3.9990 chunk 486 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48606 Z= 0.203 Angle : 0.524 8.095 66004 Z= 0.281 Chirality : 0.039 0.158 7459 Planarity : 0.004 0.051 8233 Dihedral : 13.096 164.749 7191 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.55 % Allowed : 12.69 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 5669 helix: 1.00 (0.11), residues: 2361 sheet: -1.30 (0.18), residues: 729 loop : -1.02 (0.13), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.004 0.001 HIS V 512 PHE 0.018 0.001 PHE A 23 TYR 0.011 0.001 TYR V 427 ARG 0.007 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 292 time to evaluate : 6.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8275 (mptp) cc_final: 0.8016 (tptt) REVERT: A 34 MET cc_start: 0.9123 (tmm) cc_final: 0.8834 (ppp) REVERT: A 524 MET cc_start: 0.8600 (mmm) cc_final: 0.8356 (mmm) REVERT: A 673 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8685 (mm-40) REVERT: A 677 ASN cc_start: 0.9229 (m-40) cc_final: 0.8960 (m-40) REVERT: A 868 MET cc_start: 0.8900 (ttm) cc_final: 0.8622 (ttm) REVERT: A 961 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8796 (tm-30) REVERT: A 1228 MET cc_start: 0.8617 (ttm) cc_final: 0.8065 (mtt) REVERT: A 1412 MET cc_start: 0.8193 (tmm) cc_final: 0.7960 (tmm) REVERT: B 508 MET cc_start: 0.8911 (mmt) cc_final: 0.8646 (mmm) REVERT: B 529 MET cc_start: 0.8758 (mmm) cc_final: 0.8419 (mmm) REVERT: B 550 MET cc_start: 0.9114 (tmm) cc_final: 0.8808 (tmm) REVERT: B 728 MET cc_start: 0.8897 (mtm) cc_final: 0.8620 (mtm) REVERT: B 791 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8585 (mm-30) REVERT: B 908 MET cc_start: 0.8743 (ppp) cc_final: 0.8464 (ppp) REVERT: B 1048 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.9015 (m-80) REVERT: B 1089 MET cc_start: 0.8501 (mmm) cc_final: 0.8004 (mmp) REVERT: F 109 TYR cc_start: 0.8523 (m-10) cc_final: 0.8133 (m-10) REVERT: H 123 MET cc_start: 0.9248 (ttp) cc_final: 0.8639 (tmm) REVERT: I 75 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8250 (t0) REVERT: I 78 LEU cc_start: 0.9353 (mt) cc_final: 0.9041 (mt) REVERT: U 126 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: U 264 MET cc_start: 0.5119 (mmt) cc_final: 0.4881 (mmt) outliers start: 79 outliers final: 70 residues processed: 356 average time/residue: 1.2677 time to fit residues: 728.8396 Evaluate side-chains 362 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 289 time to evaluate : 5.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Y residue 57 PHE Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain W residue 58 MET Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 360 LEU Chi-restraints excluded: chain W residue 419 ARG Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain V residue 235 CYS Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain V residue 306 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 126 GLU Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 170 LYS Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 187 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 512 optimal weight: 0.7980 chunk 337 optimal weight: 7.9990 chunk 544 optimal weight: 0.7980 chunk 332 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 378 optimal weight: 0.9990 chunk 570 optimal weight: 2.9990 chunk 525 optimal weight: 7.9990 chunk 454 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 351 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 GLN ** V 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 48606 Z= 0.157 Angle : 0.504 8.161 66004 Z= 0.267 Chirality : 0.039 0.159 7459 Planarity : 0.004 0.051 8233 Dihedral : 12.994 163.851 7191 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.26 % Allowed : 12.91 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 5669 helix: 1.28 (0.11), residues: 2364 sheet: -1.17 (0.18), residues: 729 loop : -0.81 (0.13), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.005 0.001 HIS V 512 PHE 0.028 0.001 PHE A 23 TYR 0.011 0.001 TYR V 427 ARG 0.005 0.000 ARG B 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 73 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 304 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 LYS cc_start: 0.8248 (mptp) cc_final: 0.7997 (tptt) REVERT: W 155 TRP cc_start: 0.8270 (m100) cc_final: 0.8064 (m100) REVERT: A 34 MET cc_start: 0.9125 (tmm) cc_final: 0.8839 (ppp) REVERT: A 246 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9181 (pm20) REVERT: A 673 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8631 (mm-40) REVERT: A 677 ASN cc_start: 0.9210 (m-40) cc_final: 0.8945 (m-40) REVERT: A 868 MET cc_start: 0.8858 (ttm) cc_final: 0.8585 (ttm) REVERT: A 961 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 1228 MET cc_start: 0.8602 (ttm) cc_final: 0.8124 (mtt) REVERT: A 1412 MET cc_start: 0.8204 (tmm) cc_final: 0.7968 (tmm) REVERT: A 1459 MET cc_start: 0.9423 (ptp) cc_final: 0.8954 (ptp) REVERT: B 508 MET cc_start: 0.8890 (mmt) cc_final: 0.8647 (mmm) REVERT: B 529 MET cc_start: 0.8714 (mmm) cc_final: 0.8406 (mmm) REVERT: B 550 MET cc_start: 0.9126 (tmm) cc_final: 0.8811 (tmm) REVERT: B 728 MET cc_start: 0.8892 (mtm) cc_final: 0.8608 (mtm) REVERT: B 791 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 1048 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8946 (m-80) REVERT: B 1089 MET cc_start: 0.8483 (mmm) cc_final: 0.7959 (mmp) REVERT: B 1124 ILE cc_start: 0.9016 (mm) cc_final: 0.8384 (pt) REVERT: H 123 MET cc_start: 0.9213 (ttp) cc_final: 0.8662 (tmm) REVERT: I 75 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8272 (t0) REVERT: I 78 LEU cc_start: 0.9356 (mt) cc_final: 0.9044 (mt) REVERT: U 126 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: U 264 MET cc_start: 0.5125 (mmt) cc_final: 0.4873 (mmt) outliers start: 64 outliers final: 54 residues processed: 355 average time/residue: 1.2349 time to fit residues: 706.1556 Evaluate side-chains 354 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 296 time to evaluate : 5.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain W residue 58 MET Chi-restraints excluded: chain W residue 152 HIS Chi-restraints excluded: chain W residue 174 PHE Chi-restraints excluded: chain W residue 360 LEU Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 536 GLU Chi-restraints excluded: chain V residue 235 CYS Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 957 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain U residue 126 GLU Chi-restraints excluded: chain U residue 130 GLU Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 187 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 278 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 419 optimal weight: 0.0980 chunk 67 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 467 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.088607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.072546 restraints weight = 1209766.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.072156 restraints weight = 457751.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.072959 restraints weight = 258833.477| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 48606 Z= 0.293 Angle : 0.553 7.589 66004 Z= 0.299 Chirality : 0.039 0.172 7459 Planarity : 0.004 0.051 8233 Dihedral : 13.005 160.725 7191 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.28 % Allowed : 12.92 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5669 helix: 1.10 (0.11), residues: 2361 sheet: -1.26 (0.18), residues: 722 loop : -1.01 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 453 HIS 0.005 0.001 HIS G 9 PHE 0.021 0.001 PHE A 23 TYR 0.013 0.001 TYR B 160 ARG 0.004 0.000 ARG B 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15813.55 seconds wall clock time: 276 minutes 49.64 seconds (16609.64 seconds total)