Starting phenix.real_space_refine on Sat Apr 13 17:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhg_42280/04_2024/8uhg_42280_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhg_42280/04_2024/8uhg_42280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhg_42280/04_2024/8uhg_42280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhg_42280/04_2024/8uhg_42280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhg_42280/04_2024/8uhg_42280_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhg_42280/04_2024/8uhg_42280_neut.pdb" } resolution = 2.7 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= 0.085 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 8 6.06 5 P 80 5.49 5 Mg 1 5.21 5 S 262 5.16 5 C 28152 2.51 5 N 7810 2.21 5 O 8571 1.98 5 H 44423 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1416": not complete - not flipped Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 89307 Number of models: 1 Model: "" Number of chains: 26 Chain: "X" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 283 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "V" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 8912 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 523} Chain: "W" Number of atoms: 8362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8362 Classifications: {'peptide': 526} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 22303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1399, 22303 Classifications: {'peptide': 1399} Link IDs: {'PCIS': 3, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 18193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 18193 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4031 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: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2710 Classifications: {'peptide': 171} Modifications used: {'COO': 1, '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: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1789 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1064 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1863 Classifications: {'peptide': 115} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 752 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 856 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "T" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1207 Classifications: {'DNA': 38} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 37} Chain: "U" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3054 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain breaks: 1 Chain: "Z" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4387 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 3 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18488 SG CYS A 71 114.761 56.813 76.111 1.00180.50 S ATOM 18529 SG CYS A 74 110.498 58.288 75.017 1.00181.64 S ATOM 19100 SG CYS A 111 102.054 68.903 120.507 1.00199.98 S ATOM 19150 SG CYS A 114 99.550 66.794 119.984 1.00198.81 S ATOM 19809 SG CYS A 154 97.936 69.482 121.456 1.00205.23 S ATOM 19848 SG CYS A 184 100.335 67.371 123.394 1.00202.14 S ATOM 57170 SG CYS B1119 97.360 59.400 82.923 1.00189.52 S ATOM 57214 SG CYS B1122 99.709 60.815 85.287 1.00187.72 S ATOM 57439 SG CYS B1137 101.226 58.178 83.556 1.00192.36 S ATOM 57480 SG CYS B1140 99.182 57.545 85.686 1.00191.54 S ATOM 59434 SG CYS C 88 134.097 90.553 18.644 1.00120.65 S ATOM 59459 SG CYS C 90 135.795 88.344 21.006 1.00126.17 S ATOM 59520 SG CYS C 94 137.664 90.361 17.980 1.00116.57 S ATOM 59560 SG CYS C 97 136.182 92.120 21.375 1.00114.99 S ATOM 73943 SG CYS I 17 142.158 118.075 139.669 1.00154.51 S ATOM 73985 SG CYS I 20 142.164 114.855 137.975 1.00155.14 S ATOM 74306 SG CYS I 39 138.945 116.215 138.748 1.00158.61 S ATOM 74355 SG CYS I 42 142.190 114.745 141.482 1.00160.10 S ATOM 75029 SG CYS I 86 143.157 150.077 107.809 1.00132.41 S ATOM 75078 SG CYS I 89 146.721 150.918 106.991 1.00126.43 S ATOM 75470 SG CYS I 114 145.247 147.983 105.526 1.00124.44 S ATOM 75535 SG CYS I 119 146.096 148.420 109.381 1.00128.78 S ATOM 75758 SG CYS J 7 138.517 116.681 40.887 1.00 94.67 S ATOM 75802 SG CYS J 10 137.359 117.886 37.658 1.00 94.05 S ATOM 76327 SG CYS J 44 136.727 120.125 40.534 1.00102.10 S ATOM 76337 SG CYS J 45 139.942 119.485 38.756 1.00102.49 S ATOM 78649 SG CYS L 19 163.612 84.094 56.757 1.00117.00 S ATOM 78681 SG CYS L 22 166.949 84.361 54.521 1.00122.48 S ATOM 78912 SG CYS L 36 166.161 81.212 56.396 1.00119.72 S ATOM 78961 SG CYS L 39 166.645 83.444 57.867 1.00119.73 S Time building chain proxies: 29.93, per 1000 atoms: 0.34 Number of scatterers: 89307 At special positions: 0 Unit cell: (186.594, 202.212, 161.934, 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 8 29.99 S 262 16.00 P 80 15.00 Mg 1 11.99 O 8571 8.00 N 7810 7.00 C 28152 6.00 H 44423 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.53 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 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " 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 ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " 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 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 42 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10228 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 56 sheets defined 47.4% alpha, 15.7% beta 27 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 30.83 Creating SS restraints... Processing helix chain 'X' and resid 18 through 32 Processing helix chain 'V' and resid 5 through 9 removed outlier: 3.505A pdb=" N LEU V 8 " --> pdb=" O LEU V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 21 Processing helix chain 'V' and resid 25 through 37 Processing helix chain 'V' and resid 43 through 54 Proline residue: V 49 - end of helix removed outlier: 3.818A pdb=" N HIS V 54 " --> pdb=" O PHE V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 83 removed outlier: 4.014A pdb=" N PHE V 61 " --> pdb=" O PRO V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 101 Processing helix chain 'V' and resid 102 through 104 No H-bonds generated for 'chain 'V' and resid 102 through 104' Processing helix chain 'V' and resid 109 through 120 Processing helix chain 'V' and resid 125 through 134 Processing helix chain 'V' and resid 134 through 141 Processing helix chain 'V' and resid 142 through 153 Processing helix chain 'V' and resid 154 through 177 Proline residue: V 163 - end of helix Processing helix chain 'V' and resid 191 through 196 Processing helix chain 'V' and resid 198 through 209 removed outlier: 3.548A pdb=" N GLN V 202 " --> pdb=" O GLY V 198 " (cutoff:3.500A) Processing helix chain 'V' and resid 211 through 230 Processing helix chain 'V' and resid 232 through 248 Processing helix chain 'V' and resid 250 through 255 Processing helix chain 'V' and resid 259 through 273 removed outlier: 3.591A pdb=" N ALA V 268 " --> pdb=" O TRP V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 276 through 289 Processing helix chain 'V' and resid 297 through 305 removed outlier: 3.548A pdb=" N LEU V 305 " --> pdb=" O LEU V 301 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 removed outlier: 3.654A pdb=" N VAL V 326 " --> pdb=" O LEU V 322 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY V 327 " --> pdb=" O GLN V 323 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU V 329 " --> pdb=" O LEU V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 334 Processing helix chain 'V' and resid 335 through 350 Processing helix chain 'V' and resid 350 through 357 Processing helix chain 'V' and resid 366 through 372 Processing helix chain 'V' and resid 372 through 393 removed outlier: 3.535A pdb=" N MET V 376 " --> pdb=" O ARG V 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 408 through 418 removed outlier: 3.830A pdb=" N THR V 412 " --> pdb=" O PRO V 408 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN V 418 " --> pdb=" O PHE V 414 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 435 Processing helix chain 'V' and resid 437 through 445 Processing helix chain 'V' and resid 454 through 457 Processing helix chain 'V' and resid 458 through 469 Processing helix chain 'V' and resid 473 through 477 Processing helix chain 'V' and resid 478 through 486 removed outlier: 4.165A pdb=" N CYS V 482 " --> pdb=" O LEU V 478 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU V 485 " --> pdb=" O PHE V 481 " (cutoff:3.500A) Processing helix chain 'V' and resid 489 through 494 removed outlier: 3.826A pdb=" N ALA V 493 " --> pdb=" O PHE V 489 " (cutoff:3.500A) Processing helix chain 'V' and resid 497 through 511 removed outlier: 3.742A pdb=" N HIS V 501 " --> pdb=" O LYS V 497 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 527 Processing helix chain 'V' and resid 534 through 553 Processing helix chain 'W' and resid 39 through 53 removed outlier: 4.358A pdb=" N GLN W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS W 50 " --> pdb=" O GLU W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 73 Processing helix chain 'W' and resid 76 through 86 removed outlier: 3.779A pdb=" N ILE W 80 " --> pdb=" O PRO W 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN W 86 " --> pdb=" O LEU W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 104 Processing helix chain 'W' and resid 107 through 127 removed outlier: 3.890A pdb=" N VAL W 111 " --> pdb=" O GLU W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 139 Processing helix chain 'W' and resid 143 through 150 removed outlier: 3.930A pdb=" N GLU W 147 " --> pdb=" O PRO W 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 164 Processing helix chain 'W' and resid 169 through 181 Processing helix chain 'W' and resid 190 through 195 Processing helix chain 'W' and resid 197 through 215 Processing helix chain 'W' and resid 219 through 232 Proline residue: W 225 - end of helix removed outlier: 3.538A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 250 removed outlier: 3.547A pdb=" N GLN W 250 " --> pdb=" O SER W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 254 through 272 removed outlier: 3.718A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 284 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: 3.916A pdb=" N ILE W 328 " --> pdb=" O PRO W 324 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 343 removed outlier: 3.748A pdb=" N LYS W 343 " --> pdb=" O GLN W 339 " (cutoff:3.500A) Processing helix chain 'W' and resid 349 through 366 removed outlier: 3.766A pdb=" N HIS W 354 " --> pdb=" O GLN W 350 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS W 355 " --> pdb=" O ASP W 351 " (cutoff:3.500A) Processing helix chain 'W' and resid 383 through 399 Processing helix chain 'W' and resid 405 through 410 Processing helix chain 'W' and resid 410 through 418 Processing helix chain 'W' and resid 420 through 436 Processing helix chain 'W' and resid 450 through 462 removed outlier: 3.950A pdb=" N LEU W 454 " --> pdb=" O VAL W 450 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU W 455 " --> pdb=" O HIS W 451 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP W 456 " --> pdb=" O LEU W 452 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU W 457 " --> pdb=" O ALA W 453 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 477 removed outlier: 4.737A pdb=" N LYS W 475 " --> pdb=" O GLN W 471 " (cutoff:3.500A) Processing helix chain 'W' and resid 485 through 506 Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 526 through 541 Processing helix chain 'W' and resid 546 through 558 removed outlier: 4.788A pdb=" N LEU W 552 " --> pdb=" O ASP W 548 " (cutoff:3.500A) Proline residue: W 555 - end of helix Processing helix chain 'W' and resid 574 through 584 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.698A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.611A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.633A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.566A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 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 488 through 493 removed outlier: 3.787A 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 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.893A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.792A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.549A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 856 removed outlier: 3.744A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 869 Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.622A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.757A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.042A 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 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 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 1162 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 1196 removed outlier: 4.058A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 4.038A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.619A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 4.086A 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: 3.935A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.878A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.842A pdb=" N VAL A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.864A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.156A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.795A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 253' Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.768A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.514A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.699A 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 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' 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: 3.636A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.606A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.968A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) 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: 3.602A 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 561 Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.533A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 673 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 732 removed outlier: 3.933A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 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: 3.860A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.509A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) 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: 3.540A pdb=" N ALA C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 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 16 through 20 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.718A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.868A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.689A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.582A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.503A pdb=" N LEU E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.644A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.654A 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 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.140A 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: 3.992A 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 39 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.776A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.645A 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 53 removed outlier: 4.022A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'U' and resid 10 through 18 Processing helix chain 'U' and resid 34 through 45 removed outlier: 5.455A pdb=" N ARG U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU U 43 " --> pdb=" O ASP U 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS U 44 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 49 through 63 removed outlier: 4.272A pdb=" N LEU U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU U 63 " --> pdb=" O GLY U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 71 Processing helix chain 'U' and resid 71 through 83 Processing helix chain 'U' and resid 87 through 97 removed outlier: 3.631A pdb=" N LEU U 91 " --> pdb=" O ASP U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 131 removed outlier: 4.770A pdb=" N GLU U 126 " --> pdb=" O GLY U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 144 removed outlier: 3.560A pdb=" N LEU U 144 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 152 Processing helix chain 'U' and resid 169 through 188 removed outlier: 4.070A pdb=" N LYS U 181 " --> pdb=" O GLU U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 262 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 633 removed outlier: 3.962A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'W' and resid 367 through 370 removed outlier: 4.206A pdb=" N SER W 377 " --> pdb=" O THR W 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.448A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.230A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.971A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 7.747A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.042A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.613A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.395A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.165A 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: 6.675A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.856A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.314A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.314A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.839A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB9, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 4.147A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1338 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.555A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.137A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1211 " --> pdb=" O TYR A1176 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A1175 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC4, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 7.092A pdb=" N ARG E 172 " --> pdb=" O GLY A1409 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.710A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 65 through 67 removed outlier: 9.035A pdb=" N LYS U 255 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 91 " --> pdb=" O LYS U 255 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD2, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.683A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD5, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.452A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.876A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.876A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE1, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.126A pdb=" N LYS B 821 " --> pdb=" O GLN B 825 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 825 " --> pdb=" O LYS B 821 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.188A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.598A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.786A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.469A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.469A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.812A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 2 through 13 removed outlier: 7.131A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AF1, first strand: chain 'G' and resid 149 through 153 removed outlier: 3.781A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AF3, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AF4, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'Z' and resid 453 through 454 removed outlier: 3.641A pdb=" N ARG Z 469 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.334A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.332A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AG1, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.766A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 742 through 746 removed outlier: 7.041A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 2078 hydrogen bonds defined for protein. 5841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 41.18 Time building geometry restraints manager: 57.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 44331 1.03 - 1.24: 5222 1.24 - 1.44: 14082 1.44 - 1.65: 26250 1.65 - 1.85: 412 Bond restraints: 90297 Sorted by residual: bond pdb=" C PHE B 713 " pdb=" O PHE B 713 " ideal model delta sigma weight residual 1.233 1.196 0.037 4.80e-03 4.34e+04 6.05e+01 bond pdb=" CA PRO K 4 " pdb=" C PRO K 4 " ideal model delta sigma weight residual 1.517 1.563 -0.046 6.70e-03 2.23e+04 4.79e+01 bond pdb=" C ASP C 187 " pdb=" O ASP C 187 " ideal model delta sigma weight residual 1.235 1.214 0.020 4.70e-03 4.53e+04 1.89e+01 bond pdb=" CB PHE V 262 " pdb=" CG PHE V 262 " ideal model delta sigma weight residual 1.502 1.573 -0.071 2.30e-02 1.89e+03 9.65e+00 bond pdb=" C ASP U 87 " pdb=" N PRO U 88 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.19e-02 7.06e+03 9.30e+00 ... (remaining 90292 not shown) Histogram of bond angle deviations from ideal: 93.47 - 101.61: 162 101.61 - 109.76: 68366 109.76 - 117.90: 54148 117.90 - 126.04: 39844 126.04 - 134.18: 1160 Bond angle restraints: 163680 Sorted by residual: angle pdb=" O PRO K 4 " pdb=" C PRO K 4 " pdb=" N PRO K 5 " ideal model delta sigma weight residual 121.15 124.55 -3.40 4.70e-01 4.53e+00 5.23e+01 angle pdb=" C GLY W 345 " pdb=" N ALA W 346 " pdb=" CA ALA W 346 " ideal model delta sigma weight residual 121.70 131.04 -9.34 1.80e+00 3.09e-01 2.69e+01 angle pdb=" C4' U P 6 " pdb=" C3' U P 6 " pdb=" O3' U P 6 " ideal model delta sigma weight residual 109.40 116.99 -7.59 1.50e+00 4.44e-01 2.56e+01 angle pdb=" C1' C P 9 " pdb=" N1 C P 9 " pdb=" C2 C P 9 " ideal model delta sigma weight residual 118.80 132.25 -13.45 3.00e+00 1.11e-01 2.01e+01 angle pdb=" P DA T 29 " pdb=" O5' DA T 29 " pdb=" C5' DA T 29 " ideal model delta sigma weight residual 120.00 126.35 -6.35 1.50e+00 4.44e-01 1.79e+01 ... (remaining 163675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 40607 35.85 - 71.70: 1292 71.70 - 107.55: 41 107.55 - 143.40: 2 143.40 - 179.25: 6 Dihedral angle restraints: 41948 sinusoidal: 23831 harmonic: 18117 Sorted by residual: dihedral pdb=" CD ARG A1416 " pdb=" NE ARG A1416 " pdb=" CZ ARG A1416 " pdb=" NH1 ARG A1416 " ideal model delta sinusoidal sigma weight residual 0.00 178.30 -178.30 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O4' C P 9 " pdb=" C1' C P 9 " pdb=" N1 C P 9 " pdb=" C2 C P 9 " ideal model delta sinusoidal sigma weight residual -160.00 19.25 -179.25 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U P 3 " pdb=" C1' U P 3 " pdb=" N1 U P 3 " pdb=" C2 U P 3 " ideal model delta sinusoidal sigma weight residual 200.00 35.98 164.02 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 41945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 5259 0.047 - 0.094: 1364 0.094 - 0.141: 380 0.141 - 0.188: 45 0.188 - 0.235: 1 Chirality restraints: 7049 Sorted by residual: chirality pdb=" C3' U P 6 " pdb=" C4' U P 6 " pdb=" O3' U P 6 " pdb=" C2' U P 6 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL V 123 " pdb=" N VAL V 123 " pdb=" C VAL V 123 " pdb=" CB VAL V 123 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA ILE E 194 " pdb=" N ILE E 194 " pdb=" C ILE E 194 " pdb=" CB ILE E 194 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 7046 not shown) Planarity restraints: 12961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 711 " 0.396 9.50e-02 1.11e+02 1.32e-01 1.90e+01 pdb=" NE ARG Z 711 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG Z 711 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 711 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 711 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG Z 711 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG Z 711 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG Z 711 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG Z 711 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1177 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C TYR A1177 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR A1177 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A1178 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 104 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C MET A 104 " 0.049 2.00e-02 2.50e+03 pdb=" O MET A 104 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 105 " -0.016 2.00e-02 2.50e+03 ... (remaining 12958 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 11203 2.26 - 2.84: 204090 2.84 - 3.43: 241182 3.43 - 4.01: 332286 4.01 - 4.60: 504421 Nonbonded interactions: 1293182 Sorted by model distance: nonbonded pdb=" H ARG B1085 " pdb=" OP2 DA T 29 " model vdw 1.674 1.850 nonbonded pdb=" HE2 HIS B 939 " pdb=" OE1 GLU B 983 " model vdw 1.686 1.850 nonbonded pdb=" O VAL G 89 " pdb=" H ASP G 140 " model vdw 1.686 1.850 nonbonded pdb=" O VAL B 794 " pdb=" H GLY B 946 " model vdw 1.692 1.850 nonbonded pdb=" H1 DG N 40 " pdb=" O2 DC T 13 " model vdw 1.703 1.850 ... (remaining 1293177 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: 9.680 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: 1.190 Extract box with map and model: 28.940 Check model and map are aligned: 1.020 Set scattering table: 0.610 Process input model: 266.150 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 321.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 45874 Z= 0.346 Angle : 0.832 13.446 62316 Z= 0.441 Chirality : 0.046 0.235 7049 Planarity : 0.006 0.168 7771 Dihedral : 15.444 179.246 17735 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.77 % Allowed : 4.36 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.74 (0.11), residues: 5344 helix: -0.02 (0.10), residues: 2215 sheet: -1.05 (0.18), residues: 697 loop : -0.61 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1192 HIS 0.022 0.001 HIS A1417 PHE 0.024 0.002 PHE V 61 TYR 0.021 0.002 TYR V 428 ARG 0.015 0.001 ARG A1416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 320 time to evaluate : 5.275 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: X 21 LYS cc_start: 0.6782 (tptp) cc_final: 0.6514 (mmpt) REVERT: V 228 ARG cc_start: 0.7562 (ptp-170) cc_final: 0.7309 (ptm160) REVERT: V 416 GLN cc_start: 0.8279 (pt0) cc_final: 0.7900 (pp30) REVERT: A 108 ARG cc_start: 0.8808 (mtt-85) cc_final: 0.8359 (ttm-80) REVERT: A 1309 MET cc_start: 0.8614 (ttp) cc_final: 0.8329 (ttt) REVERT: D 24 LYS cc_start: 0.9194 (mmpt) cc_final: 0.8800 (pmmt) REVERT: E 72 MET cc_start: 0.9247 (ttp) cc_final: 0.8946 (ttm) REVERT: E 94 MET cc_start: 0.9303 (mtm) cc_final: 0.9031 (mtt) REVERT: E 129 GLN cc_start: 0.8877 (pp30) cc_final: 0.8520 (pm20) REVERT: G 104 MET cc_start: 0.7063 (tpp) cc_final: 0.6530 (tpp) REVERT: K 77 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9326 (t) REVERT: U 139 LEU cc_start: 0.8146 (mp) cc_final: 0.7908 (mp) outliers start: 37 outliers final: 7 residues processed: 349 average time/residue: 3.1056 time to fit residues: 1329.0708 Evaluate side-chains 236 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 5.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 469 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain Z residue 635 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 455 optimal weight: 4.9990 chunk 408 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 422 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 489 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 349 ASN A 620 HIS A1422 GLN E 35 GLN E 43 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45874 Z= 0.237 Angle : 0.571 6.919 62316 Z= 0.304 Chirality : 0.040 0.181 7049 Planarity : 0.004 0.066 7771 Dihedral : 13.925 178.637 6835 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.69 % Allowed : 8.32 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.30 (0.11), residues: 5344 helix: 0.50 (0.11), residues: 2277 sheet: -0.99 (0.18), residues: 710 loop : -0.50 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 145 HIS 0.005 0.001 HIS U 62 PHE 0.014 0.001 PHE W 342 TYR 0.017 0.001 TYR B 916 ARG 0.008 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 5.436 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: X 21 LYS cc_start: 0.6873 (tptp) cc_final: 0.6622 (mmpt) REVERT: V 97 LEU cc_start: 0.1949 (OUTLIER) cc_final: 0.1688 (tm) REVERT: V 416 GLN cc_start: 0.8415 (pt0) cc_final: 0.8018 (pp30) REVERT: A 108 ARG cc_start: 0.8932 (mtt-85) cc_final: 0.8384 (ttm-80) REVERT: A 340 LYS cc_start: 0.9225 (ttmm) cc_final: 0.8981 (ttmm) REVERT: A 1309 MET cc_start: 0.8667 (ttp) cc_final: 0.8377 (ttt) REVERT: A 1484 MET cc_start: 0.7967 (pmm) cc_final: 0.7718 (ppp) REVERT: B 791 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8285 (tp30) REVERT: D 24 LYS cc_start: 0.9216 (mmpt) cc_final: 0.8917 (pmmt) REVERT: E 72 MET cc_start: 0.9262 (ttp) cc_final: 0.8955 (ttm) REVERT: E 129 GLN cc_start: 0.8848 (pp30) cc_final: 0.8494 (pm20) REVERT: F 80 MET cc_start: 0.8580 (mmm) cc_final: 0.7841 (mmm) REVERT: G 104 MET cc_start: 0.7014 (tpp) cc_final: 0.6265 (tpp) outliers start: 33 outliers final: 15 residues processed: 257 average time/residue: 2.8020 time to fit residues: 902.0448 Evaluate side-chains 233 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 469 LEU Chi-restraints excluded: chain V residue 501 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain Z residue 635 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 407 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 490 optimal weight: 10.0000 chunk 529 optimal weight: 20.0000 chunk 436 optimal weight: 7.9990 chunk 486 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 393 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 45874 Z= 0.466 Angle : 0.617 11.973 62316 Z= 0.332 Chirality : 0.041 0.159 7049 Planarity : 0.004 0.073 7771 Dihedral : 13.749 179.654 6829 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 0.90 % Allowed : 8.93 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.33 (0.11), residues: 5344 helix: 0.55 (0.11), residues: 2286 sheet: -1.05 (0.18), residues: 698 loop : -0.60 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 27 HIS 0.005 0.001 HIS A 84 PHE 0.023 0.001 PHE V 221 TYR 0.015 0.001 TYR V 215 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 5.432 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: X 21 LYS cc_start: 0.6997 (tptp) cc_final: 0.6666 (mmpt) REVERT: V 97 LEU cc_start: 0.1968 (OUTLIER) cc_final: 0.1683 (tm) REVERT: V 416 GLN cc_start: 0.8503 (pt0) cc_final: 0.7976 (pp30) REVERT: V 521 GLU cc_start: 0.6894 (tp30) cc_final: 0.6559 (tm-30) REVERT: A 108 ARG cc_start: 0.8974 (mtt-85) cc_final: 0.8416 (ttm-80) REVERT: A 1309 MET cc_start: 0.8707 (ttp) cc_final: 0.8424 (ttt) REVERT: A 1484 MET cc_start: 0.8147 (pmm) cc_final: 0.7893 (ppp) REVERT: B 842 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.8221 (m-70) REVERT: B 918 PHE cc_start: 0.9518 (OUTLIER) cc_final: 0.9194 (p90) REVERT: B 1151 MET cc_start: 0.8836 (ptp) cc_final: 0.8608 (ptp) REVERT: D 24 LYS cc_start: 0.9202 (mmpt) cc_final: 0.8937 (pmmt) REVERT: E 72 MET cc_start: 0.9270 (ttp) cc_final: 0.8980 (ttm) REVERT: E 129 GLN cc_start: 0.8947 (pp30) cc_final: 0.8559 (pm20) outliers start: 43 outliers final: 23 residues processed: 249 average time/residue: 2.7728 time to fit residues: 868.2930 Evaluate side-chains 233 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 501 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 484 optimal weight: 6.9990 chunk 368 optimal weight: 0.9980 chunk 254 optimal weight: 0.5980 chunk 54 optimal weight: 30.0000 chunk 234 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 492 optimal weight: 6.9990 chunk 521 optimal weight: 40.0000 chunk 257 optimal weight: 7.9990 chunk 466 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45874 Z= 0.194 Angle : 0.526 7.200 62316 Z= 0.278 Chirality : 0.039 0.157 7049 Planarity : 0.004 0.053 7771 Dihedral : 13.604 179.681 6823 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.83 % Allowed : 9.57 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.02 (0.12), residues: 5344 helix: 0.83 (0.11), residues: 2287 sheet: -0.94 (0.19), residues: 652 loop : -0.46 (0.13), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.004 0.001 HIS A 620 PHE 0.017 0.001 PHE A1202 TYR 0.013 0.001 TYR V 215 ARG 0.005 0.000 ARG U 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 5.626 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: X 21 LYS cc_start: 0.6891 (tptp) cc_final: 0.6616 (mmpt) REVERT: V 97 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.1600 (tm) REVERT: V 416 GLN cc_start: 0.8494 (pt0) cc_final: 0.7986 (pp30) REVERT: V 521 GLU cc_start: 0.6613 (tp30) cc_final: 0.6337 (tm-30) REVERT: A 271 ARG cc_start: 0.3708 (OUTLIER) cc_final: 0.3430 (tpt170) REVERT: A 1309 MET cc_start: 0.8650 (ttp) cc_final: 0.8357 (ttt) REVERT: B 842 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8213 (m-70) REVERT: B 918 PHE cc_start: 0.9480 (OUTLIER) cc_final: 0.9174 (p90) REVERT: B 1151 MET cc_start: 0.8954 (ptp) cc_final: 0.8723 (ptp) REVERT: D 24 LYS cc_start: 0.9198 (mmpt) cc_final: 0.8948 (pmmt) REVERT: E 72 MET cc_start: 0.9254 (ttp) cc_final: 0.8979 (ttm) REVERT: E 129 GLN cc_start: 0.8929 (pp30) cc_final: 0.8553 (pm20) REVERT: F 80 MET cc_start: 0.8624 (mmm) cc_final: 0.8214 (mmm) outliers start: 40 outliers final: 18 residues processed: 246 average time/residue: 2.8654 time to fit residues: 890.4096 Evaluate side-chains 234 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 5.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 501 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain Z residue 543 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 433 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 387 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 444 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 467 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1422 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 45874 Z= 0.312 Angle : 0.545 8.333 62316 Z= 0.289 Chirality : 0.040 0.235 7049 Planarity : 0.004 0.051 7771 Dihedral : 13.527 179.956 6822 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.00 % Allowed : 9.78 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.02 (0.12), residues: 5344 helix: 0.91 (0.11), residues: 2289 sheet: -0.97 (0.19), residues: 640 loop : -0.48 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.008 0.001 HIS Z 737 PHE 0.013 0.001 PHE W 201 TYR 0.016 0.001 TYR V 215 ARG 0.006 0.000 ARG V 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 5.428 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: X 21 LYS cc_start: 0.7040 (tptp) cc_final: 0.6704 (mmpt) REVERT: V 97 LEU cc_start: 0.1930 (OUTLIER) cc_final: 0.1628 (tm) REVERT: V 416 GLN cc_start: 0.8505 (pt0) cc_final: 0.7965 (pp30) REVERT: V 521 GLU cc_start: 0.6633 (tp30) cc_final: 0.6356 (tm-30) REVERT: V 537 VAL cc_start: 0.1502 (OUTLIER) cc_final: 0.0975 (p) REVERT: A 275 ASP cc_start: 0.9065 (m-30) cc_final: 0.8678 (m-30) REVERT: A 1309 MET cc_start: 0.8670 (ttp) cc_final: 0.8374 (ttt) REVERT: B 918 PHE cc_start: 0.9488 (OUTLIER) cc_final: 0.9145 (p90) REVERT: B 1151 MET cc_start: 0.9040 (ptp) cc_final: 0.8782 (ptp) REVERT: D 24 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8966 (pmmt) REVERT: E 72 MET cc_start: 0.9253 (ttp) cc_final: 0.8967 (ttm) REVERT: E 129 GLN cc_start: 0.8988 (pp30) cc_final: 0.8598 (pm20) REVERT: Z 635 MET cc_start: 0.5979 (tpp) cc_final: 0.5765 (tmm) outliers start: 48 outliers final: 24 residues processed: 253 average time/residue: 2.7275 time to fit residues: 871.0626 Evaluate side-chains 241 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 5.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 537 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 175 optimal weight: 0.8980 chunk 469 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 521 optimal weight: 2.9990 chunk 432 optimal weight: 30.0000 chunk 241 optimal weight: 9.9990 chunk 43 optimal weight: 40.0000 chunk 172 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 37 ASN V 220 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 45874 Z= 0.255 Angle : 0.529 8.220 62316 Z= 0.279 Chirality : 0.040 0.156 7049 Planarity : 0.004 0.049 7771 Dihedral : 13.451 179.992 6822 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.86 % Allowed : 10.34 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.17 (0.12), residues: 5344 helix: 1.06 (0.11), residues: 2284 sheet: -0.93 (0.19), residues: 646 loop : -0.41 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.005 0.001 HIS V 501 PHE 0.013 0.001 PHE W 201 TYR 0.015 0.001 TYR V 215 ARG 0.010 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 5.330 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: X 21 LYS cc_start: 0.7035 (tptp) cc_final: 0.6705 (mmpt) REVERT: V 97 LEU cc_start: 0.1901 (OUTLIER) cc_final: 0.1590 (tm) REVERT: V 106 MET cc_start: -0.1943 (OUTLIER) cc_final: -0.2255 (mtp) REVERT: V 416 GLN cc_start: 0.8502 (pt0) cc_final: 0.7961 (pp30) REVERT: V 521 GLU cc_start: 0.6642 (tp30) cc_final: 0.6362 (tm-30) REVERT: A 108 ARG cc_start: 0.8985 (mtt-85) cc_final: 0.8413 (ttm-80) REVERT: A 275 ASP cc_start: 0.9104 (m-30) cc_final: 0.8726 (m-30) REVERT: A 1309 MET cc_start: 0.8691 (ttp) cc_final: 0.8391 (ttt) REVERT: B 1151 MET cc_start: 0.9059 (ptp) cc_final: 0.8773 (ptp) REVERT: D 24 LYS cc_start: 0.9195 (mmpt) cc_final: 0.8984 (pmmt) REVERT: E 72 MET cc_start: 0.9232 (ttp) cc_final: 0.8963 (ttm) REVERT: E 129 GLN cc_start: 0.9011 (pp30) cc_final: 0.8632 (pm20) REVERT: Z 635 MET cc_start: 0.5951 (tpp) cc_final: 0.5736 (tmm) outliers start: 41 outliers final: 24 residues processed: 248 average time/residue: 2.6912 time to fit residues: 843.8171 Evaluate side-chains 241 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 5.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 106 MET Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 502 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 297 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 519 optimal weight: 50.0000 chunk 325 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 220 GLN V 323 GLN A 62 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 45874 Z= 0.303 Angle : 0.535 8.591 62316 Z= 0.283 Chirality : 0.039 0.155 7049 Planarity : 0.004 0.051 7771 Dihedral : 13.408 179.309 6822 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.88 % Allowed : 10.45 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.20 (0.12), residues: 5344 helix: 1.12 (0.11), residues: 2283 sheet: -0.92 (0.19), residues: 647 loop : -0.43 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.005 0.001 HIS A 472 PHE 0.013 0.001 PHE B 918 TYR 0.016 0.001 TYR V 215 ARG 0.002 0.000 ARG V 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 220 time to evaluate : 5.406 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: X 21 LYS cc_start: 0.7050 (tptp) cc_final: 0.6713 (mmpt) REVERT: V 97 LEU cc_start: 0.1910 (OUTLIER) cc_final: 0.1596 (tm) REVERT: V 416 GLN cc_start: 0.8501 (pt0) cc_final: 0.7959 (pp30) REVERT: V 521 GLU cc_start: 0.6592 (tp30) cc_final: 0.6305 (tm-30) REVERT: A 275 ASP cc_start: 0.9171 (m-30) cc_final: 0.8812 (m-30) REVERT: A 1309 MET cc_start: 0.8670 (ttp) cc_final: 0.8379 (ttt) REVERT: A 1451 MET cc_start: 0.9093 (tpp) cc_final: 0.8866 (mmm) REVERT: B 918 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9141 (p90) REVERT: E 72 MET cc_start: 0.9240 (ttp) cc_final: 0.8965 (ttm) REVERT: E 129 GLN cc_start: 0.9023 (pp30) cc_final: 0.8650 (pm20) REVERT: G 104 MET cc_start: 0.6528 (mmm) cc_final: 0.5667 (tpp) REVERT: Z 635 MET cc_start: 0.5871 (tpp) cc_final: 0.5646 (tmm) outliers start: 42 outliers final: 27 residues processed: 249 average time/residue: 2.7474 time to fit residues: 865.4845 Evaluate side-chains 244 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 5.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 303 MET Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 422 CYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 321 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 353 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 408 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 220 GLN V 431 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45874 Z= 0.227 Angle : 0.524 10.085 62316 Z= 0.274 Chirality : 0.039 0.156 7049 Planarity : 0.004 0.120 7771 Dihedral : 13.370 179.227 6822 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.77 % Allowed : 10.78 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.34 (0.12), residues: 5344 helix: 1.24 (0.11), residues: 2282 sheet: -0.85 (0.20), residues: 634 loop : -0.36 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.004 0.001 HIS A 620 PHE 0.021 0.001 PHE W 201 TYR 0.015 0.001 TYR V 215 ARG 0.013 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 5.482 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: X 21 LYS cc_start: 0.7047 (tptp) cc_final: 0.6709 (mmpt) REVERT: V 97 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.1580 (tm) REVERT: V 416 GLN cc_start: 0.8492 (pt0) cc_final: 0.7972 (pp30) REVERT: V 521 GLU cc_start: 0.6612 (tp30) cc_final: 0.6327 (tm-30) REVERT: A 248 MET cc_start: 0.9441 (ttp) cc_final: 0.8946 (ttp) REVERT: A 275 ASP cc_start: 0.9192 (m-30) cc_final: 0.8836 (m-30) REVERT: A 1309 MET cc_start: 0.8652 (ttp) cc_final: 0.8380 (ttt) REVERT: B 230 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6026 (tpp-160) REVERT: B 918 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9123 (p90) REVERT: E 72 MET cc_start: 0.9236 (ttp) cc_final: 0.8971 (ttm) REVERT: E 121 MET cc_start: 0.9030 (ppp) cc_final: 0.8585 (ppp) REVERT: E 129 GLN cc_start: 0.9015 (pp30) cc_final: 0.8671 (pm20) REVERT: G 104 MET cc_start: 0.6645 (mmm) cc_final: 0.5758 (tpp) REVERT: Z 635 MET cc_start: 0.5940 (tpp) cc_final: 0.5710 (tmm) outliers start: 37 outliers final: 25 residues processed: 245 average time/residue: 2.7110 time to fit residues: 846.2477 Evaluate side-chains 245 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 422 CYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 472 optimal weight: 2.9990 chunk 497 optimal weight: 3.9990 chunk 454 optimal weight: 3.9990 chunk 484 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 380 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 437 optimal weight: 0.9990 chunk 457 optimal weight: 9.9990 chunk 482 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 220 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 45874 Z= 0.300 Angle : 0.540 10.903 62316 Z= 0.283 Chirality : 0.039 0.158 7049 Planarity : 0.004 0.063 7771 Dihedral : 13.355 179.284 6822 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.71 % Allowed : 10.84 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.32 (0.12), residues: 5344 helix: 1.25 (0.11), residues: 2283 sheet: -0.89 (0.19), residues: 649 loop : -0.40 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.004 0.001 HIS V 260 PHE 0.014 0.001 PHE V 262 TYR 0.015 0.001 TYR V 215 ARG 0.005 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 5.650 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: X 21 LYS cc_start: 0.7083 (tptp) cc_final: 0.6735 (mmpt) REVERT: V 97 LEU cc_start: 0.1909 (OUTLIER) cc_final: 0.1590 (tm) REVERT: V 416 GLN cc_start: 0.8499 (pt0) cc_final: 0.8020 (pp30) REVERT: V 521 GLU cc_start: 0.6556 (tp30) cc_final: 0.6290 (tm-30) REVERT: A 145 TYR cc_start: 0.9137 (t80) cc_final: 0.8906 (t80) REVERT: A 248 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.8934 (ttp) REVERT: A 275 ASP cc_start: 0.9239 (m-30) cc_final: 0.8887 (m-30) REVERT: A 1309 MET cc_start: 0.8666 (ttp) cc_final: 0.8380 (ttt) REVERT: B 230 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6053 (tpp-160) REVERT: B 918 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9160 (p90) REVERT: E 72 MET cc_start: 0.9242 (ttp) cc_final: 0.8986 (ttm) REVERT: E 121 MET cc_start: 0.9053 (ppp) cc_final: 0.8574 (ppp) REVERT: E 129 GLN cc_start: 0.9017 (pp30) cc_final: 0.8680 (pm20) REVERT: G 104 MET cc_start: 0.6581 (mmm) cc_final: 0.5744 (tpp) REVERT: Z 635 MET cc_start: 0.5916 (tpp) cc_final: 0.5694 (tmm) outliers start: 34 outliers final: 26 residues processed: 244 average time/residue: 2.7772 time to fit residues: 863.7253 Evaluate side-chains 249 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 5.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 303 MET Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 422 CYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 317 optimal weight: 0.9980 chunk 511 optimal weight: 7.9990 chunk 312 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 355 optimal weight: 7.9990 chunk 536 optimal weight: 7.9990 chunk 494 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 220 GLN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45874 Z= 0.207 Angle : 0.521 11.518 62316 Z= 0.271 Chirality : 0.039 0.156 7049 Planarity : 0.003 0.048 7771 Dihedral : 13.315 178.872 6822 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.71 % Allowed : 10.89 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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 (0.12), residues: 5344 helix: 1.37 (0.11), residues: 2286 sheet: -0.80 (0.20), residues: 638 loop : -0.33 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 27 HIS 0.004 0.001 HIS V 260 PHE 0.016 0.001 PHE V 262 TYR 0.017 0.001 TYR V 215 ARG 0.004 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10688 Ramachandran restraints generated. 5344 Oldfield, 0 Emsley, 5344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 224 time to evaluate : 5.517 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: X 21 LYS cc_start: 0.7067 (tptp) cc_final: 0.6729 (mmpt) REVERT: V 97 LEU cc_start: 0.1911 (OUTLIER) cc_final: 0.1584 (tm) REVERT: V 416 GLN cc_start: 0.8509 (pt0) cc_final: 0.8051 (pp30) REVERT: V 521 GLU cc_start: 0.6547 (tp30) cc_final: 0.6285 (tm-30) REVERT: W 149 MET cc_start: -0.2691 (mtt) cc_final: -0.3103 (mmm) REVERT: A 248 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8968 (ttp) REVERT: A 275 ASP cc_start: 0.9242 (m-30) cc_final: 0.8855 (m-30) REVERT: A 1309 MET cc_start: 0.8634 (ttp) cc_final: 0.8357 (ttt) REVERT: B 918 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9181 (p90) REVERT: E 72 MET cc_start: 0.9239 (ttp) cc_final: 0.8964 (ttm) REVERT: E 121 MET cc_start: 0.9033 (ppp) cc_final: 0.8574 (ppp) REVERT: E 129 GLN cc_start: 0.9006 (pp30) cc_final: 0.8695 (pm20) REVERT: G 104 MET cc_start: 0.6647 (mmm) cc_final: 0.5731 (tpp) REVERT: Z 635 MET cc_start: 0.5892 (tpp) cc_final: 0.5660 (tmm) outliers start: 34 outliers final: 28 residues processed: 249 average time/residue: 2.6903 time to fit residues: 854.6698 Evaluate side-chains 250 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 162 SER Chi-restraints excluded: chain V residue 303 MET Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 422 CYS Chi-restraints excluded: chain W residue 180 SER Chi-restraints excluded: chain W residue 500 MET Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 339 optimal weight: 1.9990 chunk 455 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 394 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 439 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 220 GLN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.099602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.066721 restraints weight = 580735.153| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.14 r_work: 0.3066 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 45874 Z= 0.268 Angle : 0.533 12.013 62316 Z= 0.278 Chirality : 0.039 0.155 7049 Planarity : 0.003 0.051 7771 Dihedral : 13.304 179.547 6822 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.69 % Allowed : 11.03 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.43 (0.12), residues: 5344 helix: 1.36 (0.11), residues: 2286 sheet: -0.84 (0.19), residues: 654 loop : -0.35 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.004 0.001 HIS V 260 PHE 0.014 0.001 PHE V 262 TYR 0.016 0.001 TYR V 215 ARG 0.004 0.000 ARG D 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21739.59 seconds wall clock time: 375 minutes 28.26 seconds (22528.26 seconds total)