Starting phenix.real_space_refine on Sat Apr 13 17:47:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui0_42285/04_2024/8ui0_42285_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui0_42285/04_2024/8ui0_42285.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/8ui0_42285/04_2024/8ui0_42285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui0_42285/04_2024/8ui0_42285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui0_42285/04_2024/8ui0_42285_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui0_42285/04_2024/8ui0_42285_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 81 5.49 5 Mg 1 5.21 5 S 262 5.16 5 C 28162 2.51 5 N 7815 2.21 5 O 8577 1.98 5 H 44435 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 "W PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1416": not complete - not flipped Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 89341 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: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 508 Classifications: {'RNA': 16} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain breaks: 1 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 71 114.776 56.759 76.132 1.00182.25 S ATOM 18529 SG CYS A 74 110.497 58.255 75.077 1.00183.95 S ATOM 19100 SG CYS A 111 102.068 68.952 120.510 1.00200.78 S ATOM 19150 SG CYS A 114 99.585 66.854 120.012 1.00199.40 S ATOM 19809 SG CYS A 154 97.957 69.471 121.472 1.00206.61 S ATOM 19848 SG CYS A 184 100.273 67.378 123.325 1.00203.65 S ATOM 57170 SG CYS B1119 97.351 59.380 82.908 1.00189.51 S ATOM 57214 SG CYS B1122 99.583 60.692 85.218 1.00187.67 S ATOM 57439 SG CYS B1137 101.146 58.191 83.519 1.00192.52 S ATOM 57480 SG CYS B1140 99.314 57.714 85.741 1.00192.44 S ATOM 59434 SG CYS C 88 134.099 90.567 18.633 1.00122.04 S ATOM 59459 SG CYS C 90 135.788 88.346 20.993 1.00127.12 S ATOM 59520 SG CYS C 94 137.670 90.363 17.984 1.00118.21 S ATOM 59560 SG CYS C 97 136.184 92.121 21.365 1.00116.59 S ATOM 73943 SG CYS I 17 142.056 118.061 139.682 1.00154.64 S ATOM 73985 SG CYS I 20 142.182 114.922 138.103 1.00155.41 S ATOM 74306 SG CYS I 39 138.948 116.243 138.734 1.00159.47 S ATOM 74355 SG CYS I 42 142.200 114.717 141.440 1.00161.17 S ATOM 75029 SG CYS I 86 143.160 150.114 107.819 1.00132.47 S ATOM 75078 SG CYS I 89 146.732 150.943 106.958 1.00127.14 S ATOM 75470 SG CYS I 114 145.230 148.017 105.523 1.00124.26 S ATOM 75535 SG CYS I 119 146.150 148.458 109.386 1.00128.64 S ATOM 75758 SG CYS J 7 138.472 116.654 40.839 1.00 94.60 S ATOM 75802 SG CYS J 10 137.378 117.888 37.750 1.00 94.03 S ATOM 76327 SG CYS J 44 136.725 120.107 40.564 1.00101.87 S ATOM 76337 SG CYS J 45 139.936 119.462 38.744 1.00102.32 S ATOM 78649 SG CYS L 19 163.574 84.113 56.774 1.00117.95 S ATOM 78681 SG CYS L 22 166.969 84.365 54.525 1.00124.21 S ATOM 78912 SG CYS L 36 166.254 81.185 56.474 1.00121.21 S ATOM 78961 SG CYS L 39 166.822 83.574 57.831 1.00121.76 S Time building chain proxies: 29.46, per 1000 atoms: 0.33 Number of scatterers: 89341 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 81 15.00 Mg 1 11.99 O 8577 8.00 N 7815 7.00 C 28162 6.00 H 44435 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: 58.71 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 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " 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 B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " 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 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " 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 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " 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: 225 helices and 56 sheets defined 47.3% alpha, 15.6% beta 27 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 32.90 Creating SS restraints... Processing helix chain 'X' and resid 18 through 32 Processing helix chain 'V' and resid 5 through 9 removed outlier: 3.514A 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: 3.791A pdb=" N HIS V 54 " --> pdb=" O PHE V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 83 removed outlier: 3.988A 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: 3.543A 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: 3.601A 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: 3.535A pdb=" N LEU V 305 " --> pdb=" O LEU V 301 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 removed outlier: 3.672A pdb=" N VAL V 326 " --> pdb=" O LEU V 322 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY V 327 " --> pdb=" O GLN V 323 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.519A pdb=" N MET V 376 " --> pdb=" O ARG V 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 408 through 418 removed outlier: 3.801A pdb=" N THR V 412 " --> pdb=" O PRO V 408 " (cutoff:3.500A) removed outlier: 3.510A 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: 4.139A pdb=" N CYS V 482 " --> pdb=" O LEU V 478 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU V 485 " --> pdb=" O PHE V 481 " (cutoff:3.500A) Processing helix chain 'V' and resid 489 through 494 removed outlier: 3.820A pdb=" N ALA V 493 " --> pdb=" O PHE V 489 " (cutoff:3.500A) Processing helix chain 'V' and resid 497 through 511 removed outlier: 3.752A 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: 4.376A 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: 3.791A pdb=" N ILE W 80 " --> pdb=" O PRO W 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) removed outlier: 3.983A 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: 3.883A 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: 3.920A 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 182 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: 3.540A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 250 removed outlier: 3.539A pdb=" N GLN W 250 " --> pdb=" O SER W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 254 through 272 removed outlier: 3.720A 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: 3.934A pdb=" N ILE W 328 " --> pdb=" O PRO W 324 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 343 removed outlier: 3.769A pdb=" N LYS W 343 " --> pdb=" O GLN W 339 " (cutoff:3.500A) Processing helix chain 'W' and resid 349 through 366 removed outlier: 3.778A pdb=" N HIS W 354 " --> pdb=" O GLN W 350 " (cutoff:3.500A) removed outlier: 4.717A 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: 3.941A pdb=" N LEU W 454 " --> pdb=" O VAL W 450 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU W 455 " --> pdb=" O HIS W 451 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP W 456 " --> pdb=" O LEU W 452 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU W 457 " --> pdb=" O ALA W 453 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 477 removed outlier: 4.735A 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: 4.772A 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: 3.691A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.581A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.456A 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: 3.628A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.554A 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 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: 3.793A 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: 3.888A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.610A 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: 7.757A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.551A 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: 3.729A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.759A 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: 3.632A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.755A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.048A 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 1102 Proline residue: A1098 - end of helix removed outlier: 3.997A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) 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: 4.096A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.566A 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: 4.059A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.627A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.926A 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: 3.898A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.837A 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: 3.873A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.154A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.822A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.792A 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: 3.767A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.513A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.715A 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: 3.621A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.598A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.982A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.557A 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 489 through 496 removed outlier: 4.019A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.543A 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 667 through 671 removed outlier: 3.946A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.883A 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: 3.862A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.503A 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: 3.545A 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: 3.725A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.888A 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: 3.672A 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: 3.581A 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: 3.508A pdb=" N LEU E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.642A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.671A 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: 4.141A 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: 3.989A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.739A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.975A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.588A 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: 5.442A pdb=" N ARG U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) removed outlier: 5.150A 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: 4.280A pdb=" N LEU U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.632A 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: 3.621A pdb=" N LEU U 91 " --> pdb=" O ASP U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 131 removed outlier: 4.731A pdb=" N GLU U 126 " --> pdb=" O GLY U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 144 removed outlier: 3.582A 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: 4.066A 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: 3.970A 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 helix chain 'Z' and resid 641 through 643 No H-bonds generated for 'chain 'Z' and resid 641 through 643' Processing sheet with id=AA1, first strand: chain 'W' and resid 367 through 370 removed outlier: 4.197A 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: 4.453A 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: 4.244A 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: 7.785A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.449A 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: 4.043A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.610A 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: 3.627A 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: 6.408A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.932A 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: 6.863A 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: 4.339A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.596A 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: 4.339A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.343A 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: 6.838A 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: 4.170A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A1338 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.536A 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: 4.139A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1211 " --> pdb=" O TYR A1176 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.382A 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: 7.091A pdb=" N ARG E 172 " --> pdb=" O GLY A1409 " (cutoff:3.500A) removed outlier: 4.831A 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: 6.724A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.829A 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: 9.072A pdb=" N LYS U 255 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.608A 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: 3.682A 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 531 through 532 Processing sheet with id=AD6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.460A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.587A 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: 6.254A 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: 5.877A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.248A 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: 8.091A 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: 5.877A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.248A 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: 8.091A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.536A 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: 4.118A pdb=" N LYS B 821 " --> pdb=" O GLN B 825 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN B 825 " --> pdb=" O LYS B 821 " (cutoff:3.500A) removed outlier: 4.689A 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: 7.201A 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: 5.593A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.872A 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: 6.806A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.174A 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: 6.470A 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: 6.836A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.158A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.158A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.476A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.839A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'G' and resid 149 through 153 removed outlier: 3.771A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.662A 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: 7.344A 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: 7.330A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.570A 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: 6.761A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.860A 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: 7.040A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.964A 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) 2074 hydrogen bonds defined for protein. 5847 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: 45.95 Time building geometry restraints manager: 61.79 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: 44343 1.03 - 1.23: 623 1.23 - 1.43: 18447 1.43 - 1.63: 26508 1.63 - 1.84: 412 Bond restraints: 90333 Sorted by residual: bond pdb=" C5' DC T 37 " pdb=" C4' DC T 37 " ideal model delta sigma weight residual 1.518 1.581 -0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" C5 A P 18 " pdb=" C6 A P 18 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" C1' DC T 36 " pdb=" N1 DC T 36 " ideal model delta sigma weight residual 1.490 1.583 -0.093 3.00e-02 1.11e+03 9.65e+00 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 9.60e+00 bond pdb=" CA LEU J 65 " pdb=" C LEU J 65 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.41e-02 5.03e+03 9.26e+00 ... (remaining 90328 not shown) Histogram of bond angle deviations from ideal: 94.80 - 103.71: 761 103.71 - 112.62: 105899 112.62 - 121.53: 39583 121.53 - 130.43: 17248 130.43 - 139.34: 250 Bond angle restraints: 163741 Sorted by residual: angle pdb=" C GLY W 345 " pdb=" N ALA W 346 " pdb=" CA ALA W 346 " ideal model delta sigma weight residual 121.70 131.58 -9.88 1.80e+00 3.09e-01 3.02e+01 angle pdb=" C4' U P 6 " pdb=" C3' U P 6 " pdb=" O3' U P 6 " ideal model delta sigma weight residual 109.40 116.93 -7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" P DA T 29 " pdb=" O5' DA T 29 " pdb=" C5' DA T 29 " ideal model delta sigma weight residual 120.00 126.41 -6.41 1.50e+00 4.44e-01 1.83e+01 angle pdb=" CG ARG Z 711 " pdb=" CD ARG Z 711 " pdb=" NE ARG Z 711 " ideal model delta sigma weight residual 112.00 103.14 8.86 2.20e+00 2.07e-01 1.62e+01 angle pdb=" C1' DC T 37 " pdb=" C2' DC T 37 " pdb=" H2' DC T 37 " ideal model delta sigma weight residual 109.00 114.92 -5.92 1.50e+00 4.44e-01 1.56e+01 ... (remaining 163736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 40548 35.40 - 70.79: 1359 70.79 - 106.19: 45 106.19 - 141.59: 2 141.59 - 176.98: 6 Dihedral angle restraints: 41960 sinusoidal: 23843 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 -171.87 171.87 1 1.00e+01 1.00e-02 1.91e+02 dihedral pdb=" C5' A P 18 " pdb=" C4' A P 18 " pdb=" C3' A P 18 " pdb=" O3' A P 18 " ideal model delta sinusoidal sigma weight residual 147.00 80.22 66.78 1 8.00e+00 1.56e-02 9.09e+01 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 16.19 -176.19 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 41957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5447 0.050 - 0.099: 1246 0.099 - 0.149: 335 0.149 - 0.198: 23 0.198 - 0.248: 3 Chirality restraints: 7054 Sorted by residual: chirality pdb=" C2' A P 18 " pdb=" C3' A P 18 " pdb=" O2' A P 18 " pdb=" C1' A P 18 " both_signs ideal model delta sigma weight residual False -2.52 -2.77 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" P A P 18 " pdb=" OP1 A P 18 " pdb=" OP2 A P 18 " pdb=" O5' A P 18 " both_signs ideal model delta sigma weight residual True 2.41 2.63 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1' A P 18 " pdb=" O4' A P 18 " pdb=" C2' A P 18 " pdb=" N9 A P 18 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 7051 not shown) Planarity restraints: 12963 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1177 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C TYR A1177 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR A1177 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A1178 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1416 " 0.171 9.50e-02 1.11e+02 6.15e-02 6.14e+00 pdb=" NE ARG A1416 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A1416 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1416 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG A1416 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A1416 " 0.019 2.00e-02 2.50e+03 pdb="HH21 ARG A1416 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A1416 " 0.005 2.00e-02 2.50e+03 ... (remaining 12960 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 10656 2.25 - 2.84: 203294 2.84 - 3.43: 241359 3.43 - 4.01: 332083 4.01 - 4.60: 505331 Nonbonded interactions: 1292723 Sorted by model distance: nonbonded pdb=" H ARG B1085 " pdb=" OP2 DA T 29 " model vdw 1.667 1.850 nonbonded pdb="HH22 ARG A 862 " pdb=" O3' DC T 26 " model vdw 1.682 1.850 nonbonded pdb=" HE2 HIS B 939 " pdb=" OE1 GLU B 983 " model vdw 1.694 1.850 nonbonded pdb=" O VAL G 89 " pdb=" H ASP G 140 " model vdw 1.696 1.850 nonbonded pdb=" O VAL B 794 " pdb=" H GLY B 946 " model vdw 1.698 1.850 ... (remaining 1292718 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: 8.610 Set stop_for_unknowns flag: 0.020 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 1.130 Extract box with map and model: 29.290 Check model and map are aligned: 1.140 Set scattering table: 0.620 Process input model: 279.250 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.230 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 333.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 0.093 45898 Z= 0.346 Angle : 0.825 11.590 62351 Z= 0.436 Chirality : 0.046 0.248 7054 Planarity : 0.005 0.098 7772 Dihedral : 15.384 176.983 17744 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.77 % Allowed : 4.44 % Favored : 94.79 % 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: -0.69 (0.11), residues: 5344 helix: 0.04 (0.10), residues: 2210 sheet: -1.07 (0.18), residues: 700 loop : -0.60 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.008 0.001 HIS U 62 PHE 0.025 0.002 PHE V 61 TYR 0.022 0.002 TYR V 428 ARG 0.013 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 359 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 322 time to evaluate : 5.697 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: V 416 GLN cc_start: 0.8433 (pt0) cc_final: 0.8106 (pp30) REVERT: W 487 MET cc_start: 0.7468 (tpt) cc_final: 0.7081 (tmm) REVERT: A 58 MET cc_start: 0.8892 (mtp) cc_final: 0.8469 (mtp) REVERT: A 1309 MET cc_start: 0.8620 (ttp) cc_final: 0.8369 (ttt) REVERT: D 24 LYS cc_start: 0.9280 (mmpt) cc_final: 0.8677 (pmmt) REVERT: E 72 MET cc_start: 0.9262 (ttp) cc_final: 0.8959 (ttm) REVERT: E 94 MET cc_start: 0.9316 (mtm) cc_final: 0.9038 (mtt) REVERT: E 129 GLN cc_start: 0.8855 (pp30) cc_final: 0.8574 (tm130) REVERT: G 104 MET cc_start: 0.7097 (tpp) cc_final: 0.6538 (tpp) REVERT: K 77 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9322 (t) REVERT: U 139 LEU cc_start: 0.8206 (mp) cc_final: 0.7977 (mp) REVERT: U 258 ASP cc_start: 0.9165 (t0) cc_final: 0.8659 (p0) REVERT: Z 564 TYR cc_start: 0.5427 (t80) cc_final: 0.5003 (t80) outliers start: 37 outliers final: 9 residues processed: 351 average time/residue: 3.2281 time to fit residues: 1394.1874 Evaluate side-chains 236 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 226 time to evaluate : 5.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 207 MET Chi-restraints excluded: chain V residue 469 LEU Chi-restraints excluded: chain C residue 110 ASP 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: 0.9980 chunk 226 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 422 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 489 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 45898 Z= 0.274 Angle : 0.573 7.128 62351 Z= 0.307 Chirality : 0.040 0.180 7054 Planarity : 0.004 0.070 7772 Dihedral : 13.868 179.323 6849 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.77 % Allowed : 8.18 % Favored : 91.05 % 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: -0.25 (0.11), residues: 5344 helix: 0.57 (0.11), residues: 2280 sheet: -1.05 (0.18), residues: 715 loop : -0.48 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 145 HIS 0.004 0.001 HIS C 60 PHE 0.023 0.001 PHE V 221 TYR 0.015 0.001 TYR B 916 ARG 0.011 0.000 ARG B 385 *********************** 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 265 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 5.559 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: V 97 LEU cc_start: 0.1769 (OUTLIER) cc_final: 0.1509 (tm) REVERT: V 416 GLN cc_start: 0.8541 (pt0) cc_final: 0.8206 (pp30) REVERT: A 1309 MET cc_start: 0.8714 (ttp) cc_final: 0.8418 (ttt) REVERT: A 1484 MET cc_start: 0.7884 (pmm) cc_final: 0.7603 (ppp) REVERT: B 791 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8272 (tp30) REVERT: B 1161 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8796 (mt-10) REVERT: D 24 LYS cc_start: 0.9303 (mmpt) cc_final: 0.8864 (pmmt) REVERT: E 72 MET cc_start: 0.9290 (ttp) cc_final: 0.8980 (ttm) REVERT: E 129 GLN cc_start: 0.8833 (pp30) cc_final: 0.8484 (pm20) REVERT: G 104 MET cc_start: 0.7025 (tpp) cc_final: 0.6315 (tpp) REVERT: Z 564 TYR cc_start: 0.5394 (t80) cc_final: 0.5178 (t80) outliers start: 37 outliers final: 16 residues processed: 251 average time/residue: 2.7452 time to fit residues: 867.9760 Evaluate side-chains 232 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 5.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 19 THR 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 196 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 518 HIS 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 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: 4.9990 chunk 151 optimal weight: 6.9990 chunk 407 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 490 optimal weight: 10.0000 chunk 529 optimal weight: 2.9990 chunk 436 optimal weight: 9.9990 chunk 486 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 393 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 45898 Z= 0.324 Angle : 0.558 7.864 62351 Z= 0.299 Chirality : 0.040 0.159 7054 Planarity : 0.004 0.049 7772 Dihedral : 13.637 179.183 6838 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.77 % Allowed : 9.05 % 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: -0.11 (0.11), residues: 5344 helix: 0.77 (0.11), residues: 2288 sheet: -1.03 (0.19), residues: 675 loop : -0.50 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 27 HIS 0.004 0.001 HIS V 260 PHE 0.013 0.001 PHE B 918 TYR 0.016 0.001 TYR V 215 ARG 0.004 0.000 ARG V 147 *********************** 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 254 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 5.807 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: V 97 LEU cc_start: 0.1799 (OUTLIER) cc_final: 0.1516 (tm) REVERT: V 416 GLN cc_start: 0.8657 (pt0) cc_final: 0.8249 (pp30) REVERT: V 521 GLU cc_start: 0.6997 (tp30) cc_final: 0.6788 (tm-30) REVERT: A 1309 MET cc_start: 0.8699 (ttp) cc_final: 0.8421 (ttt) REVERT: A 1484 MET cc_start: 0.7920 (pmm) cc_final: 0.7713 (ppp) REVERT: B 842 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8193 (m-70) REVERT: B 918 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9127 (p90) REVERT: D 24 LYS cc_start: 0.9284 (mmpt) cc_final: 0.8876 (pmmt) REVERT: E 72 MET cc_start: 0.9290 (ttp) cc_final: 0.8981 (ttm) REVERT: E 129 GLN cc_start: 0.8907 (pp30) cc_final: 0.8541 (pm20) REVERT: G 104 MET cc_start: 0.7029 (tpp) cc_final: 0.6215 (tpp) outliers start: 37 outliers final: 20 residues processed: 241 average time/residue: 2.8385 time to fit residues: 856.2012 Evaluate side-chains 233 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 5.771 ------------------------------------------------------------------------------- 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 A residue 73 THR 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 868 MET Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 518 HIS 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 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 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: 7.9990 chunk 368 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 329 optimal weight: 3.9990 chunk 492 optimal weight: 6.9990 chunk 521 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 466 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.7751 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 45898 Z= 0.240 Angle : 0.522 7.227 62351 Z= 0.277 Chirality : 0.039 0.157 7054 Planarity : 0.004 0.048 7772 Dihedral : 13.514 179.114 6832 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.00 % Allowed : 9.20 % Favored : 89.80 % 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: 0.08 (0.12), residues: 5344 helix: 0.98 (0.11), residues: 2289 sheet: -1.01 (0.19), residues: 656 loop : -0.44 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 150 HIS 0.008 0.001 HIS V 501 PHE 0.013 0.001 PHE W 201 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 267 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 5.730 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: V 97 LEU cc_start: 0.1810 (OUTLIER) cc_final: 0.1514 (tm) REVERT: V 416 GLN cc_start: 0.8608 (pt0) cc_final: 0.8182 (pp30) REVERT: A 271 ARG cc_start: 0.3913 (mmp-170) cc_final: 0.3616 (tpt170) REVERT: A 275 ASP cc_start: 0.8954 (m-30) cc_final: 0.8585 (m-30) REVERT: A 1309 MET cc_start: 0.8666 (ttp) cc_final: 0.8389 (ttt) REVERT: B 842 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.8174 (m-70) REVERT: B 918 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9004 (p90) REVERT: B 1151 MET cc_start: 0.9017 (ptp) cc_final: 0.8801 (ptp) REVERT: D 24 LYS cc_start: 0.9268 (mmpt) cc_final: 0.8889 (pmmt) REVERT: E 72 MET cc_start: 0.9278 (ttp) cc_final: 0.8999 (ttm) REVERT: E 129 GLN cc_start: 0.8945 (pp30) cc_final: 0.8571 (pm20) REVERT: F 80 MET cc_start: 0.8656 (mmm) cc_final: 0.7974 (mmm) REVERT: G 1 MET cc_start: 0.8770 (ttm) cc_final: 0.8402 (ttm) REVERT: G 104 MET cc_start: 0.7003 (tpp) cc_final: 0.6149 (tpp) REVERT: Z 635 MET cc_start: 0.5801 (tpp) cc_final: 0.5589 (tmm) outliers start: 48 outliers final: 25 residues processed: 255 average time/residue: 2.6956 time to fit residues: 867.7562 Evaluate side-chains 238 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 5.603 ------------------------------------------------------------------------------- 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 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 1412 MET Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 594 MET 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 D residue 28 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain K residue 77 THR 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: 7.9990 chunk 295 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 387 optimal weight: 20.0000 chunk 214 optimal weight: 0.3980 chunk 444 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 467 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 45898 Z= 0.274 Angle : 0.528 7.170 62351 Z= 0.280 Chirality : 0.039 0.156 7054 Planarity : 0.004 0.048 7772 Dihedral : 13.447 179.569 6832 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 0.94 % Allowed : 9.61 % Favored : 89.45 % 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: 0.17 (0.12), residues: 5344 helix: 1.09 (0.11), residues: 2284 sheet: -0.94 (0.19), residues: 647 loop : -0.44 (0.13), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.011 0.001 HIS Z 737 PHE 0.013 0.001 PHE B 918 TYR 0.017 0.001 TYR V 215 ARG 0.003 0.000 ARG G 63 *********************** 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 262 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 5.580 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: V 97 LEU cc_start: 0.1739 (OUTLIER) cc_final: 0.1442 (tm) REVERT: V 416 GLN cc_start: 0.8634 (pt0) cc_final: 0.8203 (pp30) REVERT: W 149 MET cc_start: -0.2624 (mtt) cc_final: -0.3074 (mmm) REVERT: W 347 ARG cc_start: 0.4847 (ptm-80) cc_final: 0.4570 (ptm-80) REVERT: A 275 ASP cc_start: 0.9029 (m-30) cc_final: 0.8671 (m-30) REVERT: A 1309 MET cc_start: 0.8667 (ttp) cc_final: 0.8394 (ttt) REVERT: A 1422 GLN cc_start: 0.9022 (pt0) cc_final: 0.8820 (pp30) REVERT: A 1451 MET cc_start: 0.9090 (tpp) cc_final: 0.8827 (mmm) REVERT: B 230 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6003 (tpp-160) REVERT: B 388 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 918 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8983 (p90) REVERT: D 24 LYS cc_start: 0.9276 (mmpt) cc_final: 0.8927 (pmmt) REVERT: E 72 MET cc_start: 0.9275 (ttp) cc_final: 0.8990 (ttm) REVERT: E 129 GLN cc_start: 0.8978 (pp30) cc_final: 0.8596 (pm20) REVERT: G 1 MET cc_start: 0.8826 (ttm) cc_final: 0.8519 (ttm) REVERT: Z 635 MET cc_start: 0.5802 (tpp) cc_final: 0.5584 (tmm) outliers start: 45 outliers final: 26 residues processed: 247 average time/residue: 2.8106 time to fit residues: 886.8137 Evaluate side-chains 241 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 5.889 ------------------------------------------------------------------------------- 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 521 GLU 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 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 594 MET 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 K residue 77 THR 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: 0.7980 chunk 469 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 521 optimal weight: 9.9990 chunk 432 optimal weight: 30.0000 chunk 241 optimal weight: 8.9990 chunk 43 optimal weight: 30.0000 chunk 172 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45898 Z= 0.242 Angle : 0.517 9.275 62351 Z= 0.273 Chirality : 0.039 0.156 7054 Planarity : 0.003 0.048 7772 Dihedral : 13.392 179.771 6832 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.96 % Allowed : 10.09 % Favored : 88.95 % 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: 0.30 (0.12), residues: 5344 helix: 1.22 (0.11), residues: 2278 sheet: -0.93 (0.19), residues: 652 loop : -0.37 (0.13), residues: 2414 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 0.012 0.001 PHE B 918 TYR 0.015 0.001 TYR V 215 ARG 0.002 0.000 ARG B 416 *********************** 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 263 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 6.405 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: V 97 LEU cc_start: 0.1715 (OUTLIER) cc_final: 0.1416 (tm) REVERT: V 106 MET cc_start: -0.1916 (OUTLIER) cc_final: -0.2123 (mtp) REVERT: V 416 GLN cc_start: 0.8646 (pt0) cc_final: 0.8207 (pp30) REVERT: W 149 MET cc_start: -0.2602 (mtt) cc_final: -0.3051 (mmm) REVERT: A 275 ASP cc_start: 0.9084 (m-30) cc_final: 0.8733 (m-30) REVERT: A 1309 MET cc_start: 0.8647 (ttp) cc_final: 0.8371 (ttt) REVERT: B 388 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8225 (t80) REVERT: B 918 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8966 (p90) REVERT: D 24 LYS cc_start: 0.9287 (mmpt) cc_final: 0.8951 (pmmt) REVERT: E 72 MET cc_start: 0.9266 (ttp) cc_final: 0.8995 (ttm) REVERT: E 129 GLN cc_start: 0.8989 (pp30) cc_final: 0.8607 (pm20) REVERT: F 80 MET cc_start: 0.8284 (mmm) cc_final: 0.7967 (mmm) REVERT: G 1 MET cc_start: 0.8864 (ttm) cc_final: 0.8505 (ttm) REVERT: G 104 MET cc_start: 0.6726 (mmm) cc_final: 0.5905 (tpp) REVERT: Z 635 MET cc_start: 0.5884 (tpp) cc_final: 0.5664 (tmm) outliers start: 46 outliers final: 30 residues processed: 247 average time/residue: 2.7543 time to fit residues: 865.9215 Evaluate side-chains 249 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 5.504 ------------------------------------------------------------------------------- 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 207 MET Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 422 CYS Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain W residue 299 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 296 ASN Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 518 HIS 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 K residue 77 THR 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: 10.0000 chunk 58 optimal weight: 30.0000 chunk 297 optimal weight: 3.9990 chunk 380 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 438 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 519 optimal weight: 8.9990 chunk 325 optimal weight: 2.9990 chunk 316 optimal weight: 0.7980 chunk 239 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45898 Z= 0.224 Angle : 0.511 8.269 62351 Z= 0.268 Chirality : 0.039 0.155 7054 Planarity : 0.003 0.047 7772 Dihedral : 13.341 179.480 6832 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.90 % Allowed : 10.51 % Favored : 88.59 % 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: 0.42 (0.12), residues: 5344 helix: 1.34 (0.11), residues: 2282 sheet: -0.89 (0.19), residues: 653 loop : -0.33 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 27 HIS 0.008 0.001 HIS A 472 PHE 0.013 0.001 PHE A1388 TYR 0.023 0.001 TYR V 427 ARG 0.002 0.000 ARG B 416 *********************** 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 264 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 5.752 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: V 97 LEU cc_start: 0.1721 (OUTLIER) cc_final: 0.1418 (tm) REVERT: V 416 GLN cc_start: 0.8675 (pt0) cc_final: 0.8236 (pp30) REVERT: W 149 MET cc_start: -0.2569 (mtt) cc_final: -0.3016 (mmm) REVERT: A 248 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.8703 (ttp) REVERT: A 275 ASP cc_start: 0.9126 (m-30) cc_final: 0.8779 (m-30) REVERT: A 1309 MET cc_start: 0.8637 (ttp) cc_final: 0.8349 (ttt) REVERT: B 230 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.5993 (tpp-160) REVERT: B 388 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8207 (t80) REVERT: B 918 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8967 (p90) REVERT: D 24 LYS cc_start: 0.9283 (mmpt) cc_final: 0.8968 (pmmt) REVERT: E 72 MET cc_start: 0.9271 (ttp) cc_final: 0.9001 (ttm) REVERT: E 121 MET cc_start: 0.9033 (ppp) cc_final: 0.8631 (ppp) REVERT: E 129 GLN cc_start: 0.8987 (pp30) cc_final: 0.8637 (pm20) REVERT: G 1 MET cc_start: 0.8879 (ttm) cc_final: 0.8511 (ttm) REVERT: G 104 MET cc_start: 0.6657 (mmm) cc_final: 0.5781 (tpp) REVERT: Z 635 MET cc_start: 0.5791 (tpp) cc_final: 0.5561 (tmm) outliers start: 43 outliers final: 28 residues processed: 246 average time/residue: 2.7585 time to fit residues: 860.0926 Evaluate side-chains 247 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 5.497 ------------------------------------------------------------------------------- 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 207 MET Chi-restraints excluded: chain V residue 359 VAL Chi-restraints excluded: chain V residue 422 CYS Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain W residue 299 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 541 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 518 HIS 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 K residue 77 THR 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: 0.8980 chunk 207 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 408 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 HIS C 66 HIS ** 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: 0.7731 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45898 Z= 0.164 Angle : 0.499 9.765 62351 Z= 0.259 Chirality : 0.039 0.155 7054 Planarity : 0.003 0.045 7772 Dihedral : 13.286 179.242 6832 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.59 % 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: 0.59 (0.12), residues: 5344 helix: 1.50 (0.11), residues: 2283 sheet: -0.83 (0.19), residues: 645 loop : -0.25 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1192 HIS 0.004 0.001 HIS B1097 PHE 0.020 0.001 PHE W 201 TYR 0.022 0.001 TYR V 427 ARG 0.003 0.000 ARG B 416 *********************** 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 268 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 5.846 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: V 97 LEU cc_start: 0.1702 (OUTLIER) cc_final: 0.1398 (tm) REVERT: V 416 GLN cc_start: 0.8635 (pt0) cc_final: 0.8204 (pp30) REVERT: W 149 MET cc_start: -0.2602 (mtt) cc_final: -0.3062 (mmm) REVERT: A 248 MET cc_start: 0.9477 (mtp) cc_final: 0.8707 (ttp) REVERT: A 275 ASP cc_start: 0.9149 (m-30) cc_final: 0.8780 (m-30) REVERT: A 1309 MET cc_start: 0.8631 (ttp) cc_final: 0.8349 (ttt) REVERT: A 1451 MET cc_start: 0.9036 (tpp) cc_final: 0.8772 (mmm) REVERT: B 300 MET cc_start: 0.9441 (mmm) cc_final: 0.9218 (tpp) REVERT: B 388 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8172 (t80) REVERT: B 918 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8966 (p90) REVERT: D 24 LYS cc_start: 0.9279 (mmpt) cc_final: 0.8982 (pmmt) REVERT: E 72 MET cc_start: 0.9257 (ttp) cc_final: 0.8981 (ttm) REVERT: E 121 MET cc_start: 0.9018 (ppp) cc_final: 0.8670 (ppp) REVERT: E 129 GLN cc_start: 0.9003 (pp30) cc_final: 0.8670 (pm20) REVERT: G 1 MET cc_start: 0.8863 (ttm) cc_final: 0.8492 (ttm) REVERT: G 104 MET cc_start: 0.6756 (mmm) cc_final: 0.5790 (tpp) REVERT: I 75 ASP cc_start: 0.9077 (t0) cc_final: 0.8737 (t0) REVERT: Z 635 MET cc_start: 0.5942 (tpp) cc_final: 0.5728 (tmm) outliers start: 42 outliers final: 30 residues processed: 254 average time/residue: 2.6116 time to fit residues: 849.4520 Evaluate side-chains 250 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 5.498 ------------------------------------------------------------------------------- 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 V residue 521 GLU Chi-restraints excluded: chain W residue 180 SER Chi-restraints excluded: chain W residue 299 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 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 1412 MET Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 518 HIS 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 G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain K residue 77 THR 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: 3.9990 chunk 497 optimal weight: 6.9990 chunk 454 optimal weight: 3.9990 chunk 484 optimal weight: 0.6980 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: 6.9990 chunk 457 optimal weight: 10.0000 chunk 482 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.7772 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 45898 Z= 0.316 Angle : 0.539 10.895 62351 Z= 0.282 Chirality : 0.039 0.156 7054 Planarity : 0.004 0.062 7772 Dihedral : 13.289 179.488 6832 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.75 % Allowed : 10.91 % Favored : 88.34 % 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: 0.52 (0.12), residues: 5344 helix: 1.47 (0.11), residues: 2279 sheet: -0.84 (0.19), residues: 655 loop : -0.32 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 PHE 0.015 0.001 PHE W 201 TYR 0.022 0.001 TYR V 427 ARG 0.007 0.000 ARG V 228 *********************** 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 259 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 5.644 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: V 97 LEU cc_start: 0.1738 (OUTLIER) cc_final: 0.1435 (tm) REVERT: V 416 GLN cc_start: 0.8651 (pt0) cc_final: 0.8246 (pp30) REVERT: W 149 MET cc_start: -0.2581 (mtt) cc_final: -0.3029 (mmm) REVERT: A 145 TYR cc_start: 0.9045 (t80) cc_final: 0.8670 (t80) REVERT: A 248 MET cc_start: 0.9482 (mtp) cc_final: 0.8699 (ttp) REVERT: A 275 ASP cc_start: 0.9171 (m-30) cc_final: 0.8839 (m-30) REVERT: A 1309 MET cc_start: 0.8669 (ttp) cc_final: 0.8380 (ttt) REVERT: A 1451 MET cc_start: 0.9074 (tpp) cc_final: 0.8802 (mmm) REVERT: B 388 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8280 (t80) REVERT: B 918 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.8994 (p90) REVERT: D 24 LYS cc_start: 0.9286 (mmpt) cc_final: 0.9010 (pmmt) REVERT: E 72 MET cc_start: 0.9275 (ttp) cc_final: 0.9007 (ttm) REVERT: E 121 MET cc_start: 0.9054 (ppp) cc_final: 0.8643 (ppp) REVERT: E 129 GLN cc_start: 0.9023 (pp30) cc_final: 0.8686 (pm20) REVERT: G 1 MET cc_start: 0.8910 (ttm) cc_final: 0.8536 (ttm) REVERT: G 104 MET cc_start: 0.6701 (mmm) cc_final: 0.5766 (tpp) REVERT: Z 635 MET cc_start: 0.5738 (tpp) cc_final: 0.5508 (tmm) outliers start: 36 outliers final: 28 residues processed: 250 average time/residue: 2.7535 time to fit residues: 873.2701 Evaluate side-chains 246 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 5.470 ------------------------------------------------------------------------------- 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 W residue 180 SER Chi-restraints excluded: chain W residue 299 MET 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 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 1412 MET Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 518 HIS 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 G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain K residue 77 THR 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: 0.8980 chunk 511 optimal weight: 2.9990 chunk 312 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 355 optimal weight: 0.2980 chunk 536 optimal weight: 7.9990 chunk 494 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 330 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 358 GLN A1422 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: 0.7740 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45898 Z= 0.187 Angle : 0.514 11.955 62351 Z= 0.266 Chirality : 0.039 0.156 7054 Planarity : 0.003 0.057 7772 Dihedral : 13.258 179.023 6832 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.73 % Allowed : 11.01 % Favored : 88.26 % 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: 0.64 (0.12), residues: 5344 helix: 1.56 (0.11), residues: 2280 sheet: -0.81 (0.19), residues: 655 loop : -0.23 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.003 0.001 HIS V 260 PHE 0.014 0.001 PHE E 73 TYR 0.021 0.001 TYR V 427 ARG 0.012 0.000 ARG G 63 ********************** 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 257 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 97 LEU cc_start: 0.1733 (OUTLIER) cc_final: 0.1413 (tm) REVERT: V 416 GLN cc_start: 0.8639 (pt0) cc_final: 0.8235 (pp30) REVERT: W 149 MET cc_start: -0.2551 (mtt) cc_final: -0.3037 (mmm) REVERT: A 248 MET cc_start: 0.9491 (mtp) cc_final: 0.8793 (ttp) REVERT: A 275 ASP cc_start: 0.9177 (m-30) cc_final: 0.8837 (m-30) REVERT: A 1309 MET cc_start: 0.8599 (ttp) cc_final: 0.8317 (ttt) REVERT: A 1451 MET cc_start: 0.9074 (tpp) cc_final: 0.8815 (mmm) REVERT: B 388 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8209 (t80) REVERT: B 918 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8962 (p90) REVERT: D 24 LYS cc_start: 0.9280 (mmpt) cc_final: 0.9009 (pmmt) REVERT: E 72 MET cc_start: 0.9256 (ttp) cc_final: 0.9014 (ttm) REVERT: E 121 MET cc_start: 0.9007 (ppp) cc_final: 0.8624 (ppp) REVERT: E 129 GLN cc_start: 0.9008 (pp30) cc_final: 0.8698 (pm20) REVERT: G 1 MET cc_start: 0.8924 (ttm) cc_final: 0.8612 (ttm) REVERT: G 104 MET cc_start: 0.6761 (mmm) cc_final: 0.5720 (tpp) REVERT: I 75 ASP cc_start: 0.9081 (t0) cc_final: 0.8741 (t0) REVERT: Z 635 MET cc_start: 0.5847 (tpp) cc_final: 0.5626 (tmm) outliers start: 35 outliers final: 31 residues processed: 245 average time/residue: 2.6668 time to fit residues: 836.6308 Evaluate side-chains 253 residues out of total 4796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 5.528 ------------------------------------------------------------------------------- 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 W residue 180 SER Chi-restraints excluded: chain W residue 299 MET 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 276 LEU 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 1412 MET Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 518 HIS 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 G residue 70 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 100 PHE 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: 2.9990 chunk 130 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 439 optimal weight: 4.9990 chunk 54 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 531 ASN ** 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 = 0.4163 r_free = 0.4163 target = 0.098843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.065849 restraints weight = 582502.457| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.19 r_work: 0.3051 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 45898 Z= 0.408 Angle : 0.568 12.171 62351 Z= 0.300 Chirality : 0.040 0.155 7054 Planarity : 0.004 0.055 7772 Dihedral : 13.293 179.479 6832 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.77 % Allowed : 10.99 % Favored : 88.24 % 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: 0.45 (0.12), residues: 5344 helix: 1.41 (0.11), residues: 2274 sheet: -0.82 (0.19), residues: 663 loop : -0.37 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.005 0.001 HIS A1445 PHE 0.018 0.001 PHE U 100 TYR 0.021 0.001 TYR V 427 ARG 0.005 0.000 ARG G 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21134.60 seconds wall clock time: 365 minutes 16.66 seconds (21916.66 seconds total)