Starting phenix.real_space_refine on Sun Apr 14 15:28:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhd_42270/04_2024/8uhd_42270_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhd_42270/04_2024/8uhd_42270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhd_42270/04_2024/8uhd_42270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhd_42270/04_2024/8uhd_42270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhd_42270/04_2024/8uhd_42270_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhd_42270/04_2024/8uhd_42270_neut.pdb" } resolution = 2.8 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= 0.086 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 29857 2.51 5 N 8268 2.21 5 O 9066 1.98 5 H 47094 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 85": "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 PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 94654 Number of models: 1 Model: "" Number of chains: 28 Chain: "X" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 217 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "Z" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 7618 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 16, 'TRANS': 454} Chain breaks: 7 Chain: "W" Number of atoms: 8431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8431 Classifications: {'peptide': 530} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Chain breaks: 5 Chain: "V" Number of atoms: 8908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 8908 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 26, 'TRANS': 523} Chain: "A" Number of atoms: 22554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1416, 22554 Classifications: {'peptide': 1416} Link IDs: {'PCIS': 3, 'PTRANS': 66, 'TRANS': 1346} Chain breaks: 4 Chain: "B" Number of atoms: 18187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 18187 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4029 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "D" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3438 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 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: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1790 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1052 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: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 751 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: "P" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 4, 'rna3p': 10} 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: 3092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3092 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Chain: "Y" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1818 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 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} Chain: "Y" 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 26116 SG CYS A 71 113.702 56.780 76.445 1.00187.78 S ATOM 26157 SG CYS A 74 109.424 58.210 75.326 1.00185.27 S ATOM 26244 SG CYS A 81 112.769 60.078 75.415 1.00188.30 S ATOM 26728 SG CYS A 111 100.140 68.717 120.197 1.00209.88 S ATOM 26779 SG CYS A 114 98.310 66.443 120.321 1.00212.38 S ATOM 65032 SG CYS B1119 96.448 59.323 82.869 1.00184.58 S ATOM 65075 SG CYS B1122 99.061 60.530 85.586 1.00192.83 S ATOM 65342 SG CYS B1140 96.985 57.660 86.082 1.00191.99 S ATOM 67296 SG CYS C 88 132.795 90.732 18.935 1.00134.23 S ATOM 67320 SG CYS C 90 134.537 88.732 21.154 1.00141.17 S ATOM 67380 SG CYS C 94 136.294 90.879 18.611 1.00133.45 S ATOM 67420 SG CYS C 97 135.292 92.202 21.907 1.00130.43 S ATOM 81802 SG CYS I 17 140.281 118.590 139.545 1.00152.10 S ATOM 81845 SG CYS I 20 140.481 115.486 137.827 1.00151.73 S ATOM 82167 SG CYS I 39 137.380 116.667 138.744 1.00157.14 S ATOM 82215 SG CYS I 42 140.263 115.724 141.801 1.00151.26 S ATOM 82889 SG CYS I 86 141.890 150.696 107.892 1.00138.40 S ATOM 82938 SG CYS I 89 145.247 151.172 106.975 1.00134.16 S ATOM 83330 SG CYS I 114 144.080 148.344 105.604 1.00130.20 S ATOM 83395 SG CYS I 119 144.272 148.327 109.149 1.00139.86 S ATOM 83618 SG CYS J 7 136.989 116.732 41.314 1.00 94.41 S ATOM 83662 SG CYS J 10 136.052 118.142 37.666 1.00 95.88 S ATOM 84188 SG CYS J 44 135.505 119.889 40.690 1.00 99.13 S ATOM 84199 SG CYS J 45 138.624 119.637 38.834 1.00 99.18 S ATOM 86496 SG CYS L 19 162.337 84.388 56.943 1.00120.90 S ATOM 86528 SG CYS L 22 165.559 84.569 55.402 1.00122.98 S ATOM 86758 SG CYS L 36 164.757 81.660 56.378 1.00126.47 S ATOM 86807 SG CYS L 39 166.656 83.864 56.834 1.00126.77 S ATOM 93066 SG CYS Y 16 152.488 45.108 125.248 1.00201.27 S Time building chain proxies: 30.18, per 1000 atoms: 0.32 Number of scatterers: 94654 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 9066 8.00 N 8268 7.00 C 29857 6.00 H 47094 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS V 265 " - pdb=" SG CYS V 269 " distance=2.06 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: 60.48 Conformation dependent library (CDL) restraints added in 6.9 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 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " 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 B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " 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 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " Number of angles added : 33 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 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: 242 helices and 61 sheets defined 46.7% alpha, 16.4% beta 31 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 33.47 Creating SS restraints... Processing helix chain 'Z' and resid 188 through 203 Processing helix chain 'Z' and resid 231 through 240 removed outlier: 3.548A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 5.030A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.612A pdb=" N GLU Z 259 " --> pdb=" O PRO Z 256 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 256 through 260' Processing helix chain 'Z' and resid 341 through 349 removed outlier: 3.505A pdb=" N ILE Z 345 " --> pdb=" O ASP Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 630 through 635 removed outlier: 3.974A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) Processing helix chain 'Z' and resid 639 through 641 No H-bonds generated for 'chain 'Z' and resid 639 through 641' Processing helix chain 'W' and resid 39 through 52 Processing helix chain 'W' and resid 55 through 59 Processing helix chain 'W' and resid 61 through 73 removed outlier: 3.750A pdb=" N GLY W 73 " --> pdb=" O TYR W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 85 removed outlier: 3.656A 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 126 removed outlier: 4.107A pdb=" N VAL W 111 " --> pdb=" O GLU W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 139 removed outlier: 3.928A pdb=" N GLU W 139 " --> pdb=" O ILE W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 152 Processing helix chain 'W' and resid 152 through 166 Processing helix chain 'W' and resid 169 through 182 Processing helix chain 'W' and resid 190 through 197 removed outlier: 4.010A pdb=" N GLN W 197 " --> pdb=" O THR W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 232 removed outlier: 5.942A pdb=" N GLU W 217 " --> pdb=" O LEU W 213 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU W 218 " --> pdb=" O ASP W 214 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU W 221 " --> pdb=" O GLU W 217 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LYS W 222 " --> pdb=" O GLU W 218 " (cutoff:3.500A) Proline residue: W 225 - end of helix removed outlier: 4.280A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 250 removed outlier: 3.538A pdb=" N GLN W 250 " --> pdb=" O SER W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 254 through 272 removed outlier: 3.796A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE W 261 " --> pdb=" O ALA W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 283 removed outlier: 3.614A 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 Processing helix chain 'W' and resid 324 through 329 removed outlier: 3.727A pdb=" N ILE W 328 " --> pdb=" O PRO W 324 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 342 removed outlier: 3.563A pdb=" N PHE W 342 " --> pdb=" O MET W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 366 Processing helix chain 'W' and resid 382 through 400 removed outlier: 4.043A pdb=" N GLU W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 401 through 401 No H-bonds generated for 'chain 'W' and resid 401 through 401' Processing helix chain 'W' and resid 404 through 409 removed outlier: 3.956A 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: 3.556A pdb=" N GLU W 437 " --> pdb=" O TRP W 433 " (cutoff:3.500A) Processing helix chain 'W' and resid 450 through 462 removed outlier: 3.534A pdb=" N LEU W 455 " --> pdb=" O HIS W 451 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 479 removed outlier: 3.733A pdb=" N LYS W 475 " --> pdb=" O GLN W 471 " (cutoff:3.500A) Processing helix chain 'W' and resid 485 through 506 removed outlier: 3.643A pdb=" N ARG W 506 " --> pdb=" O HIS W 502 " (cutoff:3.500A) Processing helix chain 'W' and resid 508 through 522 removed outlier: 3.857A pdb=" N VAL W 512 " --> pdb=" O TYR W 508 " (cutoff:3.500A) Processing helix chain 'W' and resid 526 through 541 removed outlier: 3.742A pdb=" N ILE W 530 " --> pdb=" O ASP W 526 " (cutoff:3.500A) removed outlier: 3.708A 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 574 through 586 removed outlier: 3.674A pdb=" N SER W 584 " --> pdb=" O ALA W 580 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 12 through 21 Processing helix chain 'V' and resid 26 through 37 Processing helix chain 'V' and resid 41 through 54 removed outlier: 3.801A pdb=" N SER V 46 " --> pdb=" O PRO V 42 " (cutoff:3.500A) Proline residue: V 49 - end of helix removed outlier: 4.269A pdb=" N HIS V 54 " --> pdb=" O PHE V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 81 removed outlier: 4.038A pdb=" N PHE V 61 " --> pdb=" O PRO V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 102 removed outlier: 4.106A pdb=" N SER V 102 " --> pdb=" O GLU V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 119 removed outlier: 3.500A pdb=" N VAL V 113 " --> pdb=" O LEU V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 134 Processing helix chain 'V' and resid 134 through 141 Processing helix chain 'V' and resid 142 through 151 removed outlier: 3.840A pdb=" N LYS V 146 " --> pdb=" O ALA V 142 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN V 148 " --> pdb=" O GLU V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 177 removed outlier: 3.733A 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 Processing helix chain 'V' and resid 250 through 255 Processing helix chain 'V' and resid 259 through 271 removed outlier: 3.968A pdb=" N CYS V 265 " --> pdb=" O LYS V 261 " (cutoff:3.500A) Processing helix chain 'V' and resid 276 through 289 Processing helix chain 'V' and resid 295 through 306 removed outlier: 3.844A pdb=" N GLY V 299 " --> pdb=" O GLU V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 326 removed outlier: 3.655A pdb=" N VAL V 326 " --> pdb=" O LEU V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 329 No H-bonds generated for 'chain 'V' and resid 327 through 329' 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: 3.830A 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: 3.900A 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: 3.619A pdb=" N ASP V 454 " --> pdb=" O THR V 451 " (cutoff:3.500A) removed outlier: 5.962A 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: 3.932A 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: 3.502A pdb=" N THR V 492 " --> pdb=" O PHE V 489 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA V 493 " --> pdb=" O PHE V 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 489 through 493' Processing helix chain 'V' and resid 497 through 512 Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 527 Processing helix chain 'V' and resid 534 through 552 removed outlier: 3.897A pdb=" N LYS V 538 " --> pdb=" O GLY V 534 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP V 552 " --> pdb=" O LEU V 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.125A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.663A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.707A pdb=" N ILE A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.700A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.604A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 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: 3.581A 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 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.948A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.509A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.594A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 856 removed outlier: 3.725A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.655A 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 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.605A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.694A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 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 1080 removed outlier: 3.560A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1129 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: 3.782A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.594A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.562A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.918A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.582A pdb=" N VAL A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.757A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.692A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.247A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.677A 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 61 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 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 308 removed outlier: 3.531A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.636A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 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 425 removed outlier: 3.620A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.514A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) 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 563 removed outlier: 3.740A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.633A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.890A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.533A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.787A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1018 removed outlier: 3.696A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 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 removed outlier: 3.743A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.560A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.007A 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 268 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 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.695A pdb=" N SER D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) 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 removed outlier: 4.367A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.738A 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 133 through 137 removed outlier: 3.666A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 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 removed outlier: 3.527A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.544A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.103A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.975A 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 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.648A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.723A 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 39 through 52 removed outlier: 4.147A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'U' and resid 8 through 18 Processing helix chain 'U' and resid 28 through 33 Processing helix chain 'U' and resid 34 through 42 removed outlier: 4.060A 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: 3.666A 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: 3.939A 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 138 through 143 Processing helix chain 'U' and resid 145 through 153 Processing helix chain 'U' and resid 170 through 188 Processing helix chain 'U' and resid 258 through 262 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 removed outlier: 3.542A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 removed outlier: 3.526A pdb=" N ASP Y 68 " --> pdb=" O SER Y 65 " (cutoff:3.500A) No H-bonds generated for '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 sheet with id=AA1, first strand: chain 'Z' and resid 214 through 216 removed outlier: 3.797A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 372 through 377 removed outlier: 8.677A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG Z 280 " --> pdb=" O ILE Z 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id=AA4, first strand: chain 'Z' and resid 453 through 454 removed outlier: 3.564A pdb=" N ARG Z 469 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.287A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.286A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AA8, first strand: chain 'Z' and resid 636 through 638 removed outlier: 6.810A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Z' and resid 742 through 746 removed outlier: 7.082A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 367 through 370 removed outlier: 6.535A pdb=" N VAL W 367 " --> pdb=" O ILE W 378 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE W 378 " --> pdb=" O VAL W 367 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR W 369 " --> pdb=" O VAL W 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.549A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AB4, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.243A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.483A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AB7, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.914A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 7.462A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.005A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.674A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AC3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.412A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET H 37 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.835A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.377A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.377A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.831A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AD1, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.534A pdb=" N THR A1338 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.576A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.391A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AD5, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AD6, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.606A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 65 through 67 removed outlier: 9.081A pdb=" N LYS U 255 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 91 " --> pdb=" O LYS U 255 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU U 257 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 93 " --> pdb=" O LEU U 257 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AD9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AE1, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AE2, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.699A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AE4, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AE5, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.493A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.674A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.674A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE9, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.088A pdb=" N GLN B 825 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.147A 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: 5.764A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.674A pdb=" N GLN C 157 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.491A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.919A 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: 4.255A 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: 3.705A 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 removed outlier: 6.104A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 2 through 13 removed outlier: 5.883A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR G 37 " --> pdb=" O VAL G 45 " (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: 6.595A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AG3, first strand: chain 'I' and resid 24 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 Processing sheet with id=AG6, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AG7, first strand: chain 'Y' and resid 56 through 63 removed outlier: 6.981A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) 2172 hydrogen bonds defined for protein. 6081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 44.67 Time building geometry restraints manager: 63.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 46996 1.04 - 1.26: 7950 1.26 - 1.48: 18965 1.48 - 1.69: 21351 1.69 - 1.91: 438 Bond restraints: 95700 Sorted by residual: bond pdb=" C3' DC T 36 " pdb=" O3' DC T 36 " ideal model delta sigma weight residual 1.422 1.536 -0.114 3.00e-02 1.11e+03 1.45e+01 bond pdb=" CG LYS X 21 " pdb=" CD LYS X 21 " ideal model delta sigma weight residual 1.520 1.632 -0.112 3.00e-02 1.11e+03 1.40e+01 bond pdb=" C LYS W 343 " pdb=" N PRO W 344 " ideal model delta sigma weight residual 1.330 1.373 -0.042 1.19e-02 7.06e+03 1.27e+01 bond pdb=" CG LYS X 24 " pdb=" CD LYS X 24 " ideal model delta sigma weight residual 1.520 1.612 -0.092 3.00e-02 1.11e+03 9.31e+00 bond pdb=" CB CYS V 265 " pdb=" SG CYS V 265 " ideal model delta sigma weight residual 1.808 1.907 -0.099 3.30e-02 9.18e+02 8.92e+00 ... (remaining 95695 not shown) Histogram of bond angle deviations from ideal: 70.12 - 82.97: 3 82.97 - 95.83: 0 95.83 - 108.69: 39062 108.69 - 121.54: 115836 121.54 - 134.40: 18562 Bond angle restraints: 173463 Sorted by residual: angle pdb=" N ASP V 384 " pdb=" CA ASP V 384 " pdb=" HA ASP V 384 " ideal model delta sigma weight residual 110.00 70.12 39.88 3.00e+00 1.11e-01 1.77e+02 angle pdb=" CB ASP V 384 " pdb=" CA ASP V 384 " pdb=" HA ASP V 384 " ideal model delta sigma weight residual 109.00 73.99 35.01 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C ASP V 384 " pdb=" CA ASP V 384 " pdb=" HA ASP V 384 " ideal model delta sigma weight residual 109.00 79.19 29.81 3.00e+00 1.11e-01 9.87e+01 angle pdb=" CA LYS X 21 " pdb=" CB LYS X 21 " pdb=" CG LYS X 21 " ideal model delta sigma weight residual 114.10 130.21 -16.11 2.00e+00 2.50e-01 6.48e+01 angle pdb=" C3' DC T 36 " pdb=" O3' DC T 36 " pdb=" P DC T 37 " ideal model delta sigma weight residual 120.20 129.13 -8.93 1.50e+00 4.44e-01 3.55e+01 ... (remaining 173458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 42735 33.56 - 67.12: 1651 67.12 - 100.69: 90 100.69 - 134.25: 2 134.25 - 167.81: 4 Dihedral angle restraints: 44482 sinusoidal: 25231 harmonic: 19251 Sorted by residual: 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 200.00 37.60 162.40 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual -180.00 -148.72 -31.28 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA ASN A1129 " pdb=" C ASN A1129 " pdb=" N ILE A1130 " pdb=" CA ILE A1130 " ideal model delta harmonic sigma weight residual -180.00 -149.94 -30.06 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 44479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5689 0.052 - 0.104: 1356 0.104 - 0.155: 378 0.155 - 0.207: 31 0.207 - 0.259: 4 Chirality restraints: 7458 Sorted by residual: chirality pdb=" C1' A P 10 " pdb=" O4' A P 10 " pdb=" C2' A P 10 " pdb=" N9 A P 10 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASP V 384 " pdb=" N ASP V 384 " pdb=" C ASP V 384 " pdb=" CB ASP V 384 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' DC T 36 " pdb=" O4' DC T 36 " pdb=" C2' DC T 36 " pdb=" N1 DC T 36 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 7455 not shown) Planarity restraints: 13739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1138 " -0.789 9.50e-02 1.11e+02 2.64e-01 7.54e+01 pdb=" NE ARG B1138 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B1138 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B1138 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B1138 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B1138 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B1138 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B1138 " -0.010 2.00e-02 2.50e+03 pdb="HH22 ARG B1138 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER U 182 " -0.036 2.00e-02 2.50e+03 7.13e-02 5.09e+01 pdb=" C SER U 182 " 0.123 2.00e-02 2.50e+03 pdb=" O SER U 182 " -0.047 2.00e-02 2.50e+03 pdb=" N THR U 183 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 122 " -0.576 9.50e-02 1.11e+02 1.93e-01 3.98e+01 pdb=" NE ARG I 122 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG I 122 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 122 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG I 122 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG I 122 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG I 122 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG I 122 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG I 122 " -0.005 2.00e-02 2.50e+03 ... (remaining 13736 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.70: 21 1.70 - 2.43: 46104 2.43 - 3.15: 299356 3.15 - 3.88: 390692 3.88 - 4.60: 629677 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1365850 Sorted by model distance: nonbonded pdb=" HD2 ARG W 439 " pdb=" OE1 GLN W 483 " model vdw 0.979 2.620 nonbonded pdb=" H CYS B1122 " pdb="ZN ZN B1201 " model vdw 1.103 1.760 nonbonded pdb=" HE ARG W 439 " pdb=" CD GLN W 483 " model vdw 1.209 2.750 nonbonded pdb=" CD ARG W 439 " pdb=" OE1 GLN W 483 " model vdw 1.320 3.100 nonbonded pdb=" NE ARG W 439 " pdb=" OE1 GLN W 483 " model vdw 1.611 2.350 ... (remaining 1365845 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.730 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: 1.030 Extract box with map and model: 29.440 Check model and map are aligned: 1.020 Set scattering table: 0.640 Process input model: 289.810 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.220 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 344.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.006 0.114 48606 Z= 0.409 Angle : 0.915 16.106 66007 Z= 0.488 Chirality : 0.049 0.259 7458 Planarity : 0.008 0.348 8236 Dihedral : 15.568 167.811 18775 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.84 % Allowed : 4.12 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.74 (0.11), residues: 5671 helix: 0.12 (0.10), residues: 2284 sheet: -1.11 (0.18), residues: 689 loop : -0.75 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 24 HIS 0.014 0.001 HIS G 111 PHE 0.044 0.002 PHE V 387 TYR 0.019 0.002 TYR B 92 ARG 0.019 0.001 ARG B 859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 5.589 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: X 24 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7253 (mmmt) REVERT: Z 460 MET cc_start: 0.3576 (mmp) cc_final: 0.3116 (tpp) REVERT: W 58 MET cc_start: -0.0454 (mmt) cc_final: -0.0909 (mmt) REVERT: W 171 MET cc_start: 0.6823 (ttt) cc_final: 0.6554 (tpt) REVERT: V 129 LYS cc_start: 0.8533 (mttp) cc_final: 0.8215 (tptm) REVERT: A 238 MET cc_start: 0.8482 (mmt) cc_final: 0.8128 (mmm) REVERT: A 673 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: A 712 ASP cc_start: 0.8774 (m-30) cc_final: 0.8566 (m-30) REVERT: A 849 ASP cc_start: 0.9027 (m-30) cc_final: 0.8795 (m-30) REVERT: A 861 GLN cc_start: 0.9009 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 1422 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8636 (tm-30) REVERT: A 1424 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 394 ASP cc_start: 0.8543 (m-30) cc_final: 0.8320 (m-30) REVERT: B 486 ASN cc_start: 0.9122 (t0) cc_final: 0.8751 (t0) REVERT: C 62 GLU cc_start: 0.8496 (mp0) cc_final: 0.8278 (mp0) REVERT: E 168 ASN cc_start: 0.8807 (m110) cc_final: 0.8470 (m110) REVERT: H 38 ASP cc_start: 0.8290 (t70) cc_final: 0.8070 (t0) REVERT: I 100 HIS cc_start: 0.8529 (t-170) cc_final: 0.8100 (t-90) REVERT: U 145 ASN cc_start: 0.8012 (m110) cc_final: 0.7757 (m110) outliers start: 43 outliers final: 10 residues processed: 371 average time/residue: 3.0029 time to fit residues: 1392.5279 Evaluate side-chains 283 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 270 time to evaluate : 5.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain X residue 23 LYS Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain W residue 245 MET Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 673 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain L residue 39 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 0.2980 chunk 434 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 292 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 449 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 334 optimal weight: 1.9990 chunk 520 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 HIS U 80 GLN ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 48606 Z= 0.223 Angle : 0.567 9.576 66007 Z= 0.306 Chirality : 0.041 0.310 7458 Planarity : 0.004 0.069 8236 Dihedral : 13.527 174.183 7215 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 0.79 % Allowed : 7.56 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.27 (0.11), residues: 5671 helix: 0.61 (0.10), residues: 2357 sheet: -0.92 (0.18), residues: 715 loop : -0.59 (0.13), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 453 HIS 0.006 0.001 HIS W 233 PHE 0.021 0.001 PHE V 387 TYR 0.022 0.001 TYR V 138 ARG 0.009 0.000 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 5.665 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: Z 254 MET cc_start: 0.6725 (ttt) cc_final: 0.6445 (tmm) REVERT: W 58 MET cc_start: -0.0544 (mmt) cc_final: -0.1095 (mmt) REVERT: W 171 MET cc_start: 0.6904 (ttt) cc_final: 0.6366 (tpt) REVERT: W 430 TRP cc_start: 0.8807 (t60) cc_final: 0.8535 (t-100) REVERT: W 500 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8348 (mpt) REVERT: V 129 LYS cc_start: 0.8523 (mttp) cc_final: 0.8213 (tptm) REVERT: A 78 MET cc_start: 0.8989 (tpp) cc_final: 0.8732 (mmm) REVERT: A 673 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: A 861 GLN cc_start: 0.8961 (tt0) cc_final: 0.8421 (tm-30) REVERT: A 986 MET cc_start: 0.8716 (mtm) cc_final: 0.6672 (mtt) REVERT: A 1422 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 1424 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 1428 MET cc_start: 0.9098 (ttp) cc_final: 0.8370 (tmm) REVERT: A 1472 ASP cc_start: 0.8430 (m-30) cc_final: 0.8228 (m-30) REVERT: B 394 ASP cc_start: 0.8540 (m-30) cc_final: 0.8315 (m-30) REVERT: B 486 ASN cc_start: 0.9151 (t0) cc_final: 0.8901 (t0) REVERT: B 1161 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8579 (mt-10) REVERT: B 1165 MET cc_start: 0.9007 (mtm) cc_final: 0.8672 (mtm) REVERT: D 84 ARG cc_start: 0.9252 (tpp-160) cc_final: 0.8883 (tpm170) REVERT: E 94 MET cc_start: 0.9144 (mtm) cc_final: 0.8910 (mtm) REVERT: E 121 MET cc_start: 0.8577 (ptm) cc_final: 0.8285 (pmm) REVERT: E 167 GLU cc_start: 0.8477 (pm20) cc_final: 0.8200 (pm20) REVERT: E 168 ASN cc_start: 0.8622 (m110) cc_final: 0.8286 (m110) REVERT: G 63 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7814 (mmm-85) REVERT: I 100 HIS cc_start: 0.8497 (t-170) cc_final: 0.8245 (t-170) outliers start: 40 outliers final: 17 residues processed: 305 average time/residue: 2.8547 time to fit residues: 1098.1174 Evaluate side-chains 276 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 750 LEU Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 673 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 1138 ARG Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain U residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 521 optimal weight: 0.0980 chunk 563 optimal weight: 50.0000 chunk 464 optimal weight: 5.9990 chunk 516 optimal weight: 0.9990 chunk 177 optimal weight: 0.0050 chunk 418 optimal weight: 3.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 435 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 48606 Z= 0.205 Angle : 0.529 9.472 66007 Z= 0.281 Chirality : 0.040 0.313 7458 Planarity : 0.004 0.062 8236 Dihedral : 13.236 177.941 7198 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 8.70 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.08 (0.11), residues: 5671 helix: 0.98 (0.11), residues: 2369 sheet: -0.79 (0.19), residues: 709 loop : -0.47 (0.13), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 453 HIS 0.007 0.001 HIS W 233 PHE 0.017 0.001 PHE V 387 TYR 0.014 0.001 TYR B 388 ARG 0.005 0.000 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 5.710 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: Z 254 MET cc_start: 0.6810 (ttt) cc_final: 0.6604 (tmm) REVERT: W 58 MET cc_start: -0.0574 (mmt) cc_final: -0.1066 (mmt) REVERT: W 171 MET cc_start: 0.6994 (ttt) cc_final: 0.6425 (tpt) REVERT: W 430 TRP cc_start: 0.8820 (t60) cc_final: 0.8561 (t-100) REVERT: W 500 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8380 (mpt) REVERT: V 129 LYS cc_start: 0.8545 (mttp) cc_final: 0.8229 (tptm) REVERT: A 78 MET cc_start: 0.8982 (tpp) cc_final: 0.8649 (mmm) REVERT: A 334 ARG cc_start: 0.7253 (tmm-80) cc_final: 0.6982 (tmm-80) REVERT: A 861 GLN cc_start: 0.8897 (tt0) cc_final: 0.8386 (tm-30) REVERT: A 986 MET cc_start: 0.8147 (mtm) cc_final: 0.7835 (mtm) REVERT: A 1071 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: A 1422 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 1424 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 1428 MET cc_start: 0.9085 (ttp) cc_final: 0.8346 (tmm) REVERT: B 394 ASP cc_start: 0.8467 (m-30) cc_final: 0.8241 (m-30) REVERT: B 486 ASN cc_start: 0.9132 (t0) cc_final: 0.8869 (t0) REVERT: B 1161 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8580 (mt-10) REVERT: B 1165 MET cc_start: 0.8964 (mtm) cc_final: 0.8612 (mtm) REVERT: D 84 ARG cc_start: 0.9262 (tpp-160) cc_final: 0.8900 (tpm170) REVERT: G 63 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7738 (mmm-85) REVERT: K 8 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8200 (mp0) outliers start: 31 outliers final: 12 residues processed: 285 average time/residue: 2.7806 time to fit residues: 1005.7640 Evaluate side-chains 273 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 257 time to evaluate : 5.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain U residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 515 optimal weight: 4.9990 chunk 391 optimal weight: 3.9990 chunk 270 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 chunk 523 optimal weight: 3.9990 chunk 553 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 495 optimal weight: 0.0670 chunk 149 optimal weight: 30.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 616 HIS W 379 ASN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 825 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 48606 Z= 0.351 Angle : 0.554 8.933 66007 Z= 0.297 Chirality : 0.040 0.313 7458 Planarity : 0.004 0.066 8236 Dihedral : 13.023 164.173 7193 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 0.90 % Allowed : 9.47 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.10 (0.11), residues: 5671 helix: 1.04 (0.11), residues: 2370 sheet: -0.78 (0.18), residues: 725 loop : -0.51 (0.13), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 453 HIS 0.008 0.001 HIS A 432 PHE 0.022 0.001 PHE A 592 TYR 0.015 0.001 TYR B 388 ARG 0.010 0.000 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 251 time to evaluate : 5.677 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: Z 508 MET cc_start: -0.4424 (mtt) cc_final: -0.4882 (mpt) REVERT: Z 547 VAL cc_start: 0.2981 (OUTLIER) cc_final: 0.2690 (m) REVERT: W 58 MET cc_start: -0.0406 (mmt) cc_final: -0.0794 (mmp) REVERT: W 171 MET cc_start: 0.7031 (ttt) cc_final: 0.6448 (tpt) REVERT: W 430 TRP cc_start: 0.8863 (t60) cc_final: 0.8611 (t-100) REVERT: W 500 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8351 (mpt) REVERT: A 861 GLN cc_start: 0.8962 (tt0) cc_final: 0.8441 (tm-30) REVERT: A 1262 MET cc_start: 0.6663 (ptt) cc_final: 0.5852 (ptt) REVERT: A 1422 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 1424 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (p) REVERT: A 1428 MET cc_start: 0.9085 (ttp) cc_final: 0.8323 (tmm) REVERT: A 1472 ASP cc_start: 0.8505 (m-30) cc_final: 0.8285 (m-30) REVERT: B 486 ASN cc_start: 0.9164 (t0) cc_final: 0.8923 (t0) REVERT: B 1157 LEU cc_start: 0.9120 (tt) cc_final: 0.8584 (tt) REVERT: B 1161 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8553 (mt-10) REVERT: B 1165 MET cc_start: 0.8929 (mtm) cc_final: 0.8594 (mtm) REVERT: D 84 ARG cc_start: 0.9268 (tpp-160) cc_final: 0.8905 (tpm170) REVERT: E 121 MET cc_start: 0.8691 (ptm) cc_final: 0.8381 (pmm) REVERT: G 63 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7861 (mmm-85) REVERT: I 100 HIS cc_start: 0.8643 (t-170) cc_final: 0.8284 (t-90) outliers start: 46 outliers final: 25 residues processed: 285 average time/residue: 2.8900 time to fit residues: 1066.8532 Evaluate side-chains 276 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 547 VAL Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 337 PHE Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain U residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 461 optimal weight: 4.9990 chunk 314 optimal weight: 0.5980 chunk 8 optimal weight: 30.0000 chunk 412 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 472 optimal weight: 0.7980 chunk 382 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 282 optimal weight: 5.9990 chunk 497 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 551 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 48606 Z= 0.203 Angle : 0.509 7.944 66007 Z= 0.270 Chirality : 0.040 0.314 7458 Planarity : 0.004 0.054 8236 Dihedral : 12.934 162.746 7192 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.86 % Allowed : 10.08 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.31 (0.11), residues: 5671 helix: 1.25 (0.11), residues: 2375 sheet: -0.79 (0.18), residues: 726 loop : -0.39 (0.13), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.005 0.001 HIS Z 737 PHE 0.015 0.001 PHE V 387 TYR 0.027 0.001 TYR V 428 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 255 time to evaluate : 5.753 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: Z 508 MET cc_start: -0.4410 (mtt) cc_final: -0.4864 (mpt) REVERT: W 58 MET cc_start: -0.0356 (mmt) cc_final: -0.0758 (mmp) REVERT: W 430 TRP cc_start: 0.8836 (t60) cc_final: 0.8605 (t-100) REVERT: W 500 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8318 (mpt) REVERT: A 58 MET cc_start: 0.7930 (mtp) cc_final: 0.7706 (ttm) REVERT: A 861 GLN cc_start: 0.8872 (tt0) cc_final: 0.8259 (tm-30) REVERT: A 1422 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 1424 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7941 (p) REVERT: A 1428 MET cc_start: 0.9084 (ttp) cc_final: 0.8316 (tmm) REVERT: B 486 ASN cc_start: 0.9134 (t0) cc_final: 0.8895 (t0) REVERT: B 1075 MET cc_start: 0.6761 (ptm) cc_final: 0.6464 (ppp) REVERT: B 1089 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8598 (mtp) REVERT: B 1157 LEU cc_start: 0.9100 (tt) cc_final: 0.8503 (tt) REVERT: B 1161 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8530 (mt-10) REVERT: B 1165 MET cc_start: 0.8938 (mtm) cc_final: 0.8590 (mtm) REVERT: D 84 ARG cc_start: 0.9269 (tpp-160) cc_final: 0.8913 (tpm170) REVERT: E 121 MET cc_start: 0.8602 (ptm) cc_final: 0.8294 (pmm) REVERT: G 10 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7718 (mm-30) REVERT: G 63 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7768 (mmm-85) outliers start: 44 outliers final: 24 residues processed: 285 average time/residue: 2.7178 time to fit residues: 989.0435 Evaluate side-chains 272 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 185 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 186 optimal weight: 3.9990 chunk 498 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 325 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 554 optimal weight: 6.9990 chunk 460 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 183 optimal weight: 0.0470 chunk 291 optimal weight: 8.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 48606 Z= 0.235 Angle : 0.514 8.192 66007 Z= 0.271 Chirality : 0.040 0.314 7458 Planarity : 0.004 0.053 8236 Dihedral : 12.866 163.035 7192 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.88 % Allowed : 10.43 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.41 (0.11), residues: 5671 helix: 1.35 (0.11), residues: 2374 sheet: -0.77 (0.18), residues: 728 loop : -0.36 (0.13), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 278 HIS 0.006 0.001 HIS I 100 PHE 0.016 0.001 PHE A 592 TYR 0.036 0.001 TYR V 428 ARG 0.005 0.000 ARG W 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 252 time to evaluate : 5.578 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: Z 508 MET cc_start: -0.4500 (mtt) cc_final: -0.4934 (mpt) REVERT: W 58 MET cc_start: -0.0378 (mmt) cc_final: -0.0788 (mmp) REVERT: W 171 MET cc_start: 0.7957 (tmm) cc_final: 0.7389 (tpt) REVERT: W 430 TRP cc_start: 0.8855 (t60) cc_final: 0.8635 (t-100) REVERT: W 500 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8314 (mpt) REVERT: A 58 MET cc_start: 0.7925 (mtp) cc_final: 0.7651 (ttm) REVERT: A 861 GLN cc_start: 0.8877 (tt0) cc_final: 0.8316 (tm-30) REVERT: A 1422 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8473 (tm-30) REVERT: A 1424 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7984 (p) REVERT: B 486 ASN cc_start: 0.9150 (t0) cc_final: 0.8924 (t0) REVERT: B 1075 MET cc_start: 0.6767 (ptm) cc_final: 0.6471 (ppp) REVERT: B 1157 LEU cc_start: 0.9101 (tt) cc_final: 0.8520 (tt) REVERT: B 1161 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8561 (mt-10) REVERT: B 1165 MET cc_start: 0.8914 (mtm) cc_final: 0.8563 (mtm) REVERT: D 84 ARG cc_start: 0.9270 (tpp-160) cc_final: 0.8908 (tpm170) REVERT: E 121 MET cc_start: 0.8614 (ptm) cc_final: 0.8353 (pmm) REVERT: G 63 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7783 (mmm-85) outliers start: 45 outliers final: 32 residues processed: 282 average time/residue: 2.6554 time to fit residues: 962.0919 Evaluate side-chains 284 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 249 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 21 LYS Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 185 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 534 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 466 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 552 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 254 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 391 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 48606 Z= 0.268 Angle : 0.522 8.840 66007 Z= 0.275 Chirality : 0.040 0.315 7458 Planarity : 0.004 0.052 8236 Dihedral : 12.814 163.348 7192 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.04 % Allowed : 10.53 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.46 (0.11), residues: 5671 helix: 1.41 (0.11), residues: 2378 sheet: -0.78 (0.19), residues: 728 loop : -0.33 (0.13), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.004 0.001 HIS K 69 PHE 0.018 0.001 PHE A 592 TYR 0.028 0.001 TYR V 428 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 253 time to evaluate : 6.395 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: W 58 MET cc_start: -0.0416 (mmt) cc_final: -0.0922 (mmt) REVERT: W 430 TRP cc_start: 0.8876 (t60) cc_final: 0.8664 (t-100) REVERT: W 500 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8316 (mpt) REVERT: A 58 MET cc_start: 0.7919 (mtp) cc_final: 0.7659 (ttm) REVERT: A 248 MET cc_start: 0.9386 (mtp) cc_final: 0.9179 (mtp) REVERT: A 334 ARG cc_start: 0.7343 (tmm-80) cc_final: 0.6732 (tmm-80) REVERT: A 861 GLN cc_start: 0.8906 (tt0) cc_final: 0.8290 (tm-30) REVERT: A 986 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7702 (mtt) REVERT: A 1422 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 1424 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7902 (p) REVERT: B 486 ASN cc_start: 0.9171 (t0) cc_final: 0.8957 (t0) REVERT: B 1075 MET cc_start: 0.6799 (ptm) cc_final: 0.6427 (ppp) REVERT: B 1157 LEU cc_start: 0.9115 (tt) cc_final: 0.8535 (tt) REVERT: B 1161 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 1165 MET cc_start: 0.8934 (mtm) cc_final: 0.8582 (mtm) REVERT: D 84 ARG cc_start: 0.9266 (tpp-160) cc_final: 0.8913 (tpm170) REVERT: G 63 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7780 (mmm-85) outliers start: 53 outliers final: 35 residues processed: 289 average time/residue: 2.6655 time to fit residues: 991.1024 Evaluate side-chains 289 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 271 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 185 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 341 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 329 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 351 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 434 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN B 980 HIS ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 48606 Z= 0.159 Angle : 0.502 10.806 66007 Z= 0.260 Chirality : 0.040 0.315 7458 Planarity : 0.003 0.051 8236 Dihedral : 12.760 163.387 7192 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.73 % Allowed : 10.92 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.64 (0.12), residues: 5671 helix: 1.57 (0.11), residues: 2379 sheet: -0.69 (0.19), residues: 726 loop : -0.25 (0.13), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.009 0.001 HIS I 100 PHE 0.013 0.001 PHE V 387 TYR 0.019 0.001 TYR Z 226 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 5.620 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: W 58 MET cc_start: -0.0449 (mmt) cc_final: -0.0967 (mmt) REVERT: W 171 MET cc_start: 0.7933 (tmm) cc_final: 0.7136 (tpt) REVERT: W 245 MET cc_start: 0.8996 (mmp) cc_final: 0.8790 (mmp) REVERT: W 500 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8260 (mpt) REVERT: A 58 MET cc_start: 0.7854 (mtp) cc_final: 0.7591 (ttm) REVERT: A 248 MET cc_start: 0.9380 (mtp) cc_final: 0.8786 (ttp) REVERT: A 334 ARG cc_start: 0.7280 (tmm-80) cc_final: 0.6701 (tmm-80) REVERT: A 861 GLN cc_start: 0.8875 (tt0) cc_final: 0.8186 (tm-30) REVERT: A 865 ILE cc_start: 0.9548 (pp) cc_final: 0.9150 (pt) REVERT: A 1422 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 1424 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 486 ASN cc_start: 0.9138 (t0) cc_final: 0.8900 (t0) REVERT: B 1075 MET cc_start: 0.6747 (ptm) cc_final: 0.6399 (ppp) REVERT: B 1157 LEU cc_start: 0.9101 (tt) cc_final: 0.8515 (tt) REVERT: B 1161 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8572 (mt-10) REVERT: B 1165 MET cc_start: 0.8907 (mtm) cc_final: 0.8533 (mtm) REVERT: D 84 ARG cc_start: 0.9276 (tpp-160) cc_final: 0.8909 (tpm170) REVERT: E 121 MET cc_start: 0.8669 (ptm) cc_final: 0.8306 (pmm) REVERT: G 63 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7722 (mmm-85) outliers start: 37 outliers final: 28 residues processed: 280 average time/residue: 2.7719 time to fit residues: 1005.3276 Evaluate side-chains 277 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 185 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 502 optimal weight: 4.9990 chunk 529 optimal weight: 2.9990 chunk 482 optimal weight: 40.0000 chunk 514 optimal weight: 10.0000 chunk 528 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 404 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 465 optimal weight: 0.6980 chunk 486 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48606 Z= 0.227 Angle : 0.512 10.509 66007 Z= 0.267 Chirality : 0.039 0.315 7458 Planarity : 0.003 0.051 8236 Dihedral : 12.707 163.181 7192 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.82 % Allowed : 10.94 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.67 (0.12), residues: 5671 helix: 1.59 (0.11), residues: 2387 sheet: -0.68 (0.19), residues: 729 loop : -0.23 (0.13), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.007 0.001 HIS I 100 PHE 0.016 0.001 PHE A 592 TYR 0.023 0.001 TYR V 428 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 249 time to evaluate : 5.756 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: Z 260 MET cc_start: 0.1975 (mtt) cc_final: 0.1703 (mpt) REVERT: W 58 MET cc_start: -0.0337 (mmt) cc_final: -0.0850 (mmt) REVERT: W 500 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8264 (mpt) REVERT: A 58 MET cc_start: 0.7866 (mtp) cc_final: 0.7625 (ttm) REVERT: A 248 MET cc_start: 0.9378 (mtp) cc_final: 0.8794 (ttp) REVERT: A 334 ARG cc_start: 0.7298 (tmm-80) cc_final: 0.6947 (tmm-80) REVERT: A 611 ASP cc_start: 0.8460 (p0) cc_final: 0.8209 (p0) REVERT: A 861 GLN cc_start: 0.8888 (tt0) cc_final: 0.8240 (tm-30) REVERT: A 986 MET cc_start: 0.8216 (mtm) cc_final: 0.7864 (mtt) REVERT: A 1422 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8392 (tm-30) REVERT: A 1424 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7770 (p) REVERT: B 486 ASN cc_start: 0.9159 (t0) cc_final: 0.8949 (t0) REVERT: B 1075 MET cc_start: 0.6784 (ptm) cc_final: 0.6395 (ppp) REVERT: B 1151 MET cc_start: 0.9208 (ptm) cc_final: 0.8892 (ptm) REVERT: B 1157 LEU cc_start: 0.9096 (tt) cc_final: 0.8536 (tt) REVERT: B 1161 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8573 (mt-10) REVERT: B 1165 MET cc_start: 0.8916 (mtm) cc_final: 0.8582 (mtm) REVERT: D 84 ARG cc_start: 0.9253 (tpp-160) cc_final: 0.8904 (tpm170) REVERT: E 121 MET cc_start: 0.8674 (ptm) cc_final: 0.8307 (pmm) REVERT: G 63 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7744 (mmm-85) outliers start: 42 outliers final: 35 residues processed: 280 average time/residue: 2.7957 time to fit residues: 1000.2560 Evaluate side-chains 284 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain V residue 271 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1138 ARG Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 512 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 544 optimal weight: 8.9990 chunk 332 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 570 optimal weight: 7.9990 chunk 525 optimal weight: 0.9980 chunk 454 optimal weight: 0.0060 chunk 47 optimal weight: 6.9990 chunk 351 optimal weight: 3.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48606 Z= 0.221 Angle : 0.517 11.101 66007 Z= 0.268 Chirality : 0.040 0.314 7458 Planarity : 0.003 0.051 8236 Dihedral : 12.659 162.909 7192 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.77 % Allowed : 11.06 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.70 (0.12), residues: 5671 helix: 1.62 (0.11), residues: 2388 sheet: -0.65 (0.19), residues: 732 loop : -0.23 (0.13), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 453 HIS 0.004 0.001 HIS I 100 PHE 0.015 0.001 PHE A 592 TYR 0.024 0.001 TYR Z 224 ARG 0.004 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11342 Ramachandran restraints generated. 5671 Oldfield, 0 Emsley, 5671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 1132 is missing expected H atoms. Skipping. Residue LYS 942 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 249 time to evaluate : 5.739 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: Z 260 MET cc_start: 0.2142 (mtt) cc_final: 0.1863 (mpt) REVERT: W 58 MET cc_start: -0.0239 (mmt) cc_final: -0.0749 (mmt) REVERT: W 500 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8280 (mpt) REVERT: A 58 MET cc_start: 0.7856 (mtp) cc_final: 0.7611 (ttm) REVERT: A 334 ARG cc_start: 0.7278 (tmm-80) cc_final: 0.6936 (tmm-80) REVERT: A 611 ASP cc_start: 0.8476 (p0) cc_final: 0.8270 (p0) REVERT: A 861 GLN cc_start: 0.8876 (tt0) cc_final: 0.8212 (tm-30) REVERT: A 1422 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 1424 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7750 (p) REVERT: B 486 ASN cc_start: 0.9158 (t0) cc_final: 0.8952 (t0) REVERT: B 1075 MET cc_start: 0.6773 (ptm) cc_final: 0.6399 (ppp) REVERT: B 1157 LEU cc_start: 0.9099 (tt) cc_final: 0.8505 (tt) REVERT: B 1161 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8543 (mt-10) REVERT: B 1165 MET cc_start: 0.8877 (mtm) cc_final: 0.8460 (mtm) REVERT: D 84 ARG cc_start: 0.9253 (tpp-160) cc_final: 0.8900 (tpm170) REVERT: E 121 MET cc_start: 0.8687 (ptm) cc_final: 0.8311 (pmm) REVERT: G 63 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7716 (mmm-85) outliers start: 39 outliers final: 35 residues processed: 279 average time/residue: 2.7193 time to fit residues: 967.7642 Evaluate side-chains 281 residues out of total 5091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 737 HIS Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 288 SER Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 452 LEU Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 265 CYS Chi-restraints excluded: chain V residue 271 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1138 ARG Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 278 optimal weight: 7.9990 chunk 361 optimal weight: 3.9990 chunk 484 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 419 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 455 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 467 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 113 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 = 0.4130 r_free = 0.4130 target = 0.095374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062608 restraints weight = 613096.878| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.54 r_work: 0.2979 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 48606 Z= 0.306 Angle : 0.533 11.144 66007 Z= 0.279 Chirality : 0.040 0.315 7458 Planarity : 0.004 0.051 8236 Dihedral : 12.630 162.755 7192 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.84 % Allowed : 11.04 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.64 (0.12), residues: 5671 helix: 1.59 (0.11), residues: 2387 sheet: -0.67 (0.19), residues: 730 loop : -0.28 (0.13), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.013 0.001 HIS I 100 PHE 0.020 0.001 PHE A 592 TYR 0.019 0.001 TYR V 428 ARG 0.005 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21722.49 seconds wall clock time: 376 minutes 28.15 seconds (22588.15 seconds total)