Starting phenix.real_space_refine on Mon Mar 25 00:35:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amv_11824/03_2024/7amv_11824_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amv_11824/03_2024/7amv_11824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amv_11824/03_2024/7amv_11824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amv_11824/03_2024/7amv_11824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amv_11824/03_2024/7amv_11824_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amv_11824/03_2024/7amv_11824_neut.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.010 sd= 1.009 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 84 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 28784 2.51 5 N 7488 2.21 5 O 8608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 950": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B PHE 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "I TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 317": "NH1" <-> "NH2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I ARG 460": "NH1" <-> "NH2" Residue "I ARG 539": "NH1" <-> "NH2" Residue "I ARG 576": "NH1" <-> "NH2" Residue "I ARG 583": "NH1" <-> "NH2" Residue "I ARG 595": "NH1" <-> "NH2" Residue "I ARG 659": "NH1" <-> "NH2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 784": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 134": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 271": "NH1" <-> "NH2" Residue "K TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 401": "NH1" <-> "NH2" Residue "K PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 438": "NH1" <-> "NH2" Residue "K ARG 453": "NH1" <-> "NH2" Residue "K PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 511": "NH1" <-> "NH2" Residue "K ARG 533": "NH1" <-> "NH2" Residue "K TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 673": "NH1" <-> "NH2" Residue "K PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 706": "NH1" <-> "NH2" Residue "S ARG 89": "NH1" <-> "NH2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 95": "OE1" <-> "OE2" Residue "W PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 184": "OE1" <-> "OE2" Residue "W ARG 195": "NH1" <-> "NH2" Residue "W ARG 219": "NH1" <-> "NH2" Residue "W TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 238": "NH1" <-> "NH2" Residue "W ARG 263": "NH1" <-> "NH2" Residue "W ARG 334": "NH1" <-> "NH2" Residue "W TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 434": "NH1" <-> "NH2" Residue "W PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 457": "NH1" <-> "NH2" Residue "W TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 515": "OE1" <-> "OE2" Residue "W GLU 545": "OE1" <-> "OE2" Residue "W ARG 579": "NH1" <-> "NH2" Residue "W TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45172 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1248, 10017 Classifications: {'peptide': 1248} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1204} Chain breaks: 2 Chain: "B" Number of atoms: 9060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 9060 Classifications: {'peptide': 1126} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1073} Chain breaks: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1233 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "I" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5807 Classifications: {'peptide': 694} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 670} Chain breaks: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "K" Number of atoms: 5776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5776 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 25, 'TRANS': 682} Chain: "N" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 861 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "S" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1036 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "T" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 861 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "W" Number of atoms: 5207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5207 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 21, 'TRANS': 615} 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: "J" 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 360 SG CYS A 49 120.050 103.506 55.877 1.00103.12 S ATOM 382 SG CYS A 52 123.783 104.045 55.236 1.00 95.09 S ATOM 434 SG CYS A 59 122.608 100.850 56.928 1.00 90.50 S ATOM 694 SG CYS A 90 105.183 106.351 102.294 1.00106.28 S ATOM 718 SG CYS A 93 107.041 109.707 102.916 1.00107.20 S ATOM 1016 SG CYS A 130 106.990 108.284 105.806 1.00112.09 S ATOM 18486 SG CYS B1087 130.498 107.091 69.954 1.00 74.97 S ATOM 18509 SG CYS B1090 127.171 105.596 71.069 1.00 76.21 S ATOM 18598 SG CYS B1103 127.338 107.713 67.896 1.00 79.87 S ATOM 18623 SG CYS B1106 127.828 109.323 71.333 1.00 79.17 S ATOM 30984 SG CYS J 7 129.368 32.024 39.885 1.00 54.34 S ATOM 31003 SG CYS J 10 132.724 30.497 38.713 1.00 56.50 S ATOM 31240 SG CYS J 39 131.301 29.549 42.102 1.00 57.88 S ATOM 31246 SG CYS J 40 129.752 28.394 38.732 1.00 58.10 S Time building chain proxies: 22.29, per 1000 atoms: 0.49 Number of scatterers: 45172 At special positions: 0 Unit cell: (193.241, 159.487, 175.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 203 16.00 P 84 15.00 Mg 1 11.99 O 8608 8.00 N 7488 7.00 C 28784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 444 " distance=2.03 Simple disulfide: pdb=" SG CYS K 418 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 441 " - pdb=" SG CYS K 459 " distance=2.03 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: 18.58 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 15 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10254 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 64 sheets defined 43.6% alpha, 17.7% beta 19 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 14.75 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.577A pdb=" N GLY A 42 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.632A pdb=" N LYS A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.616A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 219 through 231 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.738A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.975A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 489 removed outlier: 4.049A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 489 " --> pdb=" O TYR A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.885A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 586 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.747A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.669A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.576A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.273A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.567A pdb=" N ASN A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.523A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 4.070A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1171 removed outlier: 3.925A pdb=" N TYR A1171 " --> pdb=" O MET A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 3.952A pdb=" N ASP A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.751A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.800A pdb=" N MET A1264 " --> pdb=" O LEU A1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.532A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.557A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.590A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 361 through 393 removed outlier: 3.576A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.676A pdb=" N LEU B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 465 through 470 removed outlier: 4.769A pdb=" N TYR B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 removed outlier: 3.829A pdb=" N TYR B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.924A pdb=" N GLU B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 643 through 650 Processing helix chain 'B' and resid 651 through 656 removed outlier: 4.131A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.813A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.522A pdb=" N SER B 675 " --> pdb=" O TYR B 671 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.892A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 783 through 789 Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 916 through 923 removed outlier: 4.097A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.126A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.612A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 991 Processing helix chain 'B' and resid 1021 through 1026 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.984A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.857A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.903A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.655A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.908A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 Processing helix chain 'E' and resid 98 through 101 removed outlier: 3.558A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.733A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.516A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 3 through 10 removed outlier: 4.207A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.547A pdb=" N LEU I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.849A pdb=" N SER I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG I 35 " --> pdb=" O ASP I 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN I 36 " --> pdb=" O PHE I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 40 removed outlier: 3.987A pdb=" N PHE I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 37 through 40' Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.987A pdb=" N TYR I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 65 Processing helix chain 'I' and resid 69 through 78 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.962A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 192 Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.744A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 270 through 272 No H-bonds generated for 'chain 'I' and resid 270 through 272' Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 327 through 336 removed outlier: 3.684A pdb=" N ARG I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 406 through 421 Processing helix chain 'I' and resid 428 through 454 removed outlier: 5.761A pdb=" N GLN I 448 " --> pdb=" O ASN I 444 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU I 449 " --> pdb=" O SER I 445 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 502 Processing helix chain 'I' and resid 503 through 514 removed outlier: 3.629A pdb=" N ILE I 507 " --> pdb=" O SER I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 538 Processing helix chain 'I' and resid 545 through 558 Processing helix chain 'I' and resid 561 through 581 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 689 through 694 removed outlier: 4.121A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 Processing helix chain 'I' and resid 773 through 794 removed outlier: 5.854A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 62 through 75 Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 140 through 144 Processing helix chain 'K' and resid 150 through 164 removed outlier: 3.706A pdb=" N ILE K 154 " --> pdb=" O ASP K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 200 Processing helix chain 'K' and resid 254 through 262 Processing helix chain 'K' and resid 293 through 298 removed outlier: 4.404A pdb=" N PHE K 298 " --> pdb=" O GLU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 315 No H-bonds generated for 'chain 'K' and resid 313 through 315' Processing helix chain 'K' and resid 335 through 352 removed outlier: 3.580A pdb=" N TYR K 339 " --> pdb=" O ASN K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 372 Processing helix chain 'K' and resid 411 through 413 No H-bonds generated for 'chain 'K' and resid 411 through 413' Processing helix chain 'K' and resid 431 through 439 removed outlier: 3.768A pdb=" N HIS K 435 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 461 Processing helix chain 'K' and resid 490 through 498 Processing helix chain 'K' and resid 534 through 546 Processing helix chain 'K' and resid 560 through 564 removed outlier: 3.560A pdb=" N ILE K 564 " --> pdb=" O ALA K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 598 through 603 Processing helix chain 'K' and resid 652 through 664 Proline residue: K 661 - end of helix Processing helix chain 'K' and resid 670 through 686 removed outlier: 3.569A pdb=" N PHE K 674 " --> pdb=" O ALA K 670 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS K 685 " --> pdb=" O ASN K 681 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET K 686 " --> pdb=" O ILE K 682 " (cutoff:3.500A) Processing helix chain 'K' and resid 692 through 701 removed outlier: 3.598A pdb=" N THR K 696 " --> pdb=" O ASN K 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 706 Processing helix chain 'S' and resid 24 through 32 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 69 through 79 removed outlier: 4.393A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 85 removed outlier: 3.648A pdb=" N ASN S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 109 removed outlier: 3.962A pdb=" N LYS S 108 " --> pdb=" O CYS S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.540A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 139 Processing helix chain 'S' and resid 144 through 149 removed outlier: 3.646A pdb=" N PHE S 148 " --> pdb=" O TYR S 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 9 removed outlier: 3.771A pdb=" N ILE W 6 " --> pdb=" O ASN W 2 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE W 9 " --> pdb=" O ILE W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 38 removed outlier: 3.572A pdb=" N ILE W 35 " --> pdb=" O VAL W 31 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 49 No H-bonds generated for 'chain 'W' and resid 47 through 49' Processing helix chain 'W' and resid 50 through 63 removed outlier: 3.510A pdb=" N ILE W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 74 through 92 Processing helix chain 'W' and resid 97 through 99 No H-bonds generated for 'chain 'W' and resid 97 through 99' Processing helix chain 'W' and resid 106 through 115 removed outlier: 3.948A pdb=" N ASN W 115 " --> pdb=" O SER W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 127 Processing helix chain 'W' and resid 136 through 140 Processing helix chain 'W' and resid 143 through 157 Processing helix chain 'W' and resid 172 through 183 removed outlier: 3.803A pdb=" N GLY W 176 " --> pdb=" O PRO W 172 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 202 Processing helix chain 'W' and resid 205 through 216 Processing helix chain 'W' and resid 251 through 264 Processing helix chain 'W' and resid 273 through 281 removed outlier: 3.673A pdb=" N ASN W 277 " --> pdb=" O LYS W 273 " (cutoff:3.500A) Processing helix chain 'W' and resid 284 through 289 removed outlier: 3.704A pdb=" N LEU W 288 " --> pdb=" O GLY W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 297 removed outlier: 4.317A pdb=" N PHE W 296 " --> pdb=" O LEU W 292 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 322 Processing helix chain 'W' and resid 325 through 336 removed outlier: 3.834A pdb=" N GLN W 336 " --> pdb=" O ILE W 332 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 363 removed outlier: 4.217A pdb=" N LYS W 357 " --> pdb=" O GLY W 353 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR W 358 " --> pdb=" O LEU W 354 " (cutoff:3.500A) Processing helix chain 'W' and resid 390 through 394 removed outlier: 3.506A pdb=" N LYS W 394 " --> pdb=" O SER W 391 " (cutoff:3.500A) Processing helix chain 'W' and resid 396 through 405 removed outlier: 3.650A pdb=" N LEU W 400 " --> pdb=" O SER W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 444 through 454 Processing helix chain 'W' and resid 479 through 483 removed outlier: 3.975A pdb=" N ASP W 482 " --> pdb=" O ASP W 479 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 498 removed outlier: 3.514A pdb=" N ILE W 496 " --> pdb=" O GLN W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 500 through 526 Processing helix chain 'W' and resid 538 through 554 removed outlier: 3.962A pdb=" N ASN W 553 " --> pdb=" O GLN W 549 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN W 554 " --> pdb=" O PHE W 550 " (cutoff:3.500A) Processing helix chain 'W' and resid 561 through 570 Processing helix chain 'W' and resid 574 through 589 Processing helix chain 'W' and resid 627 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.236A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 282 removed outlier: 4.038A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.570A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.245A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 removed outlier: 3.673A pdb=" N GLY A 684 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.555A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB3, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB4, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB6, first strand: chain 'A' and resid 1006 through 1012 Processing sheet with id=AB7, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.878A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.878A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.887A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.887A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.714A pdb=" N LEU B 170 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.950A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.453A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.761A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.761A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP J 61 " --> pdb=" O VAL B 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD2, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.870A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1084 through 1087 removed outlier: 4.528A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD5, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'C' and resid 37 through 43 removed outlier: 4.942A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.680A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.679A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AE2, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.453A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 90 removed outlier: 7.477A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 114 through 118 Processing sheet with id=AE5, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.183A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 161 through 166 Processing sheet with id=AE7, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AE8, first strand: chain 'I' and resid 354 through 357 Processing sheet with id=AE9, first strand: chain 'I' and resid 656 through 659 Processing sheet with id=AF1, first strand: chain 'I' and resid 668 through 671 Processing sheet with id=AF2, first strand: chain 'K' and resid 51 through 53 removed outlier: 3.653A pdb=" N VAL K 53 " --> pdb=" O TYR K 24 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU K 9 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL K 132 " --> pdb=" O LEU K 9 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU K 11 " --> pdb=" O VAL K 132 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG K 134 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N VAL K 13 " --> pdb=" O ARG K 134 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 91 through 92 Processing sheet with id=AF4, first strand: chain 'K' and resid 171 through 176 removed outlier: 3.725A pdb=" N THR K 277 " --> pdb=" O LYS K 176 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 269 through 271 Processing sheet with id=AF6, first strand: chain 'K' and resid 362 through 363 Processing sheet with id=AF7, first strand: chain 'K' and resid 399 through 401 Processing sheet with id=AF8, first strand: chain 'K' and resid 427 through 430 Processing sheet with id=AF9, first strand: chain 'K' and resid 474 through 475 Processing sheet with id=AG1, first strand: chain 'K' and resid 504 through 505 removed outlier: 6.793A pdb=" N ASN K 504 " --> pdb=" O LYS K 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY K 517 " --> pdb=" O VAL K 582 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL K 582 " --> pdb=" O GLY K 517 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS K 519 " --> pdb=" O MET K 580 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET K 580 " --> pdb=" O HIS K 519 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL K 521 " --> pdb=" O GLU K 578 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU K 578 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS K 523 " --> pdb=" O VAL K 576 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N VAL K 576 " --> pdb=" O CYS K 523 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 504 through 505 removed outlier: 6.793A pdb=" N ASN K 504 " --> pdb=" O LYS K 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY K 517 " --> pdb=" O VAL K 582 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL K 582 " --> pdb=" O GLY K 517 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS K 519 " --> pdb=" O MET K 580 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET K 580 " --> pdb=" O HIS K 519 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL K 521 " --> pdb=" O GLU K 578 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU K 578 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS K 523 " --> pdb=" O VAL K 576 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N VAL K 576 " --> pdb=" O CYS K 523 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE K 568 " --> pdb=" O VAL K 579 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE K 548 " --> pdb=" O HIS K 569 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU K 571 " --> pdb=" O ILE K 548 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE K 550 " --> pdb=" O LEU K 571 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP W 623 " --> pdb=" O PHE K 557 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 613 through 617 Processing sheet with id=AG4, first strand: chain 'W' and resid 101 through 105 removed outlier: 6.499A pdb=" N LYS W 67 " --> pdb=" O ILE W 131 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE W 133 " --> pdb=" O LYS W 67 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR W 69 " --> pdb=" O ILE W 133 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N LEU W 161 " --> pdb=" O SER W 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE W 132 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU W 163 " --> pdb=" O PHE W 132 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL W 134 " --> pdb=" O LEU W 163 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL W 41 " --> pdb=" O LEU W 162 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU W 42 " --> pdb=" O SER W 221 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR W 223 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE W 44 " --> pdb=" O TYR W 223 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 193 through 194 removed outlier: 3.954A pdb=" N LEU W 203 " --> pdb=" O SER W 194 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 233 through 236 removed outlier: 4.796A pdb=" N LEU W 472 " --> pdb=" O HIS W 236 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG W 244 " --> pdb=" O VAL W 470 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU W 472 " --> pdb=" O ARG W 244 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 233 through 236 removed outlier: 4.796A pdb=" N LEU W 472 " --> pdb=" O HIS W 236 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR W 385 " --> pdb=" O PHE W 417 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE W 419 " --> pdb=" O THR W 385 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA W 387 " --> pdb=" O PHE W 419 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER W 366 " --> pdb=" O PHE W 386 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ILE W 388 " --> pdb=" O SER W 366 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 302 through 304 removed outlier: 5.187A pdb=" N GLU W 302 " --> pdb=" O ILE W 309 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE W 309 " --> pdb=" O GLU W 302 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 378 through 379 removed outlier: 3.677A pdb=" N LYS W 382 " --> pdb=" O ILE W 379 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 557 through 558 1958 hydrogen bonds defined for protein. 5403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 24.08 Time building geometry restraints manager: 20.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13869 1.34 - 1.46: 8271 1.46 - 1.58: 23625 1.58 - 1.70: 164 1.70 - 1.82: 332 Bond restraints: 46261 Sorted by residual: bond pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.67e+00 bond pdb=" C3' DG N 59 " pdb=" O3' DG N 59 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.48e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" C3' DA N 10 " pdb=" O3' DA N 10 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.77e+00 ... (remaining 46256 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 1646 107.10 - 113.82: 25687 113.82 - 120.54: 18369 120.54 - 127.26: 16706 127.26 - 133.98: 499 Bond angle restraints: 62907 Sorted by residual: angle pdb=" CA VAL B 475 " pdb=" C VAL B 475 " pdb=" N PRO B 476 " ideal model delta sigma weight residual 116.57 119.68 -3.11 9.80e-01 1.04e+00 1.01e+01 angle pdb=" O3' DC N 54 " pdb=" C3' DC N 54 " pdb=" C2' DC N 54 " ideal model delta sigma weight residual 111.50 116.24 -4.74 1.50e+00 4.44e-01 9.97e+00 angle pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " pdb=" P DT T 13 " ideal model delta sigma weight residual 120.20 124.54 -4.34 1.50e+00 4.44e-01 8.39e+00 angle pdb=" N GLY K 14 " pdb=" CA GLY K 14 " pdb=" C GLY K 14 " ideal model delta sigma weight residual 112.13 115.99 -3.86 1.34e+00 5.57e-01 8.29e+00 angle pdb=" N LYS B1098 " pdb=" CA LYS B1098 " pdb=" C LYS B1098 " ideal model delta sigma weight residual 110.88 107.25 3.63 1.28e+00 6.10e-01 8.04e+00 ... (remaining 62902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 27423 35.10 - 70.21: 403 70.21 - 105.31: 22 105.31 - 140.42: 1 140.42 - 175.52: 5 Dihedral angle restraints: 27854 sinusoidal: 11988 harmonic: 15866 Sorted by residual: dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT T 12 " pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " pdb=" P DT T 13 " ideal model delta sinusoidal sigma weight residual 220.00 44.48 175.52 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU B 220 " pdb=" C LEU B 220 " pdb=" N ASN B 221 " pdb=" CA ASN B 221 " ideal model delta harmonic sigma weight residual 180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 27851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4772 0.034 - 0.067: 1559 0.067 - 0.101: 457 0.101 - 0.134: 317 0.134 - 0.168: 35 Chirality restraints: 7140 Sorted by residual: chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ILE K 442 " pdb=" N ILE K 442 " pdb=" C ILE K 442 " pdb=" CB ILE K 442 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE B 759 " pdb=" N ILE B 759 " pdb=" C ILE B 759 " pdb=" CB ILE B 759 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 7137 not shown) Planarity restraints: 7663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 41 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C PHE B 41 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE B 41 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.018 2.00e-02 2.50e+03 1.55e-02 4.18e+00 pdb=" CG PHE A 938 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 548 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C PHE B 548 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE B 548 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 549 " -0.011 2.00e-02 2.50e+03 ... (remaining 7660 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 522 2.64 - 3.20: 41885 3.20 - 3.77: 69287 3.77 - 4.33: 100817 4.33 - 4.90: 163861 Nonbonded interactions: 376372 Sorted by model distance: nonbonded pdb=" O ILE A 408 " pdb=" OG SER A 411 " model vdw 2.075 2.440 nonbonded pdb=" OH TYR B 798 " pdb=" OD1 ASP B 841 " model vdw 2.098 2.440 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.105 2.170 nonbonded pdb=" O PRO K 101 " pdb=" OG SER K 139 " model vdw 2.111 2.440 nonbonded pdb=" OG SER K 84 " pdb=" O ASN K 87 " model vdw 2.115 2.440 ... (remaining 376367 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.360 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 139.790 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 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:10.170 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.003 0.057 46261 Z= 0.198 Angle : 0.536 7.579 62907 Z= 0.299 Chirality : 0.043 0.168 7140 Planarity : 0.003 0.042 7663 Dihedral : 11.790 175.523 17591 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.41 % Allowed : 2.65 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 5306 helix: 1.72 (0.12), residues: 1941 sheet: -0.33 (0.18), residues: 757 loop : -0.34 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 365 HIS 0.004 0.001 HIS B 126 PHE 0.035 0.001 PHE A 938 TYR 0.013 0.001 TYR B 377 ARG 0.004 0.000 ARG K 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1071 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 THR cc_start: 0.8581 (m) cc_final: 0.8197 (t) REVERT: A 104 ASP cc_start: 0.7311 (t0) cc_final: 0.7104 (t0) REVERT: A 137 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7668 (mp10) REVERT: A 141 LYS cc_start: 0.7186 (mppt) cc_final: 0.6846 (tptt) REVERT: A 226 MET cc_start: 0.7023 (mmm) cc_final: 0.6792 (mmm) REVERT: A 249 ASP cc_start: 0.7463 (t0) cc_final: 0.6334 (p0) REVERT: A 287 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7656 (ttp-110) REVERT: A 520 ASP cc_start: 0.7474 (m-30) cc_final: 0.7235 (m-30) REVERT: A 522 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7437 (mp0) REVERT: A 604 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 617 LYS cc_start: 0.8100 (mttt) cc_final: 0.7818 (mttt) REVERT: A 858 LYS cc_start: 0.8416 (tptt) cc_final: 0.8210 (tptm) REVERT: A 936 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 1010 ARG cc_start: 0.7970 (ptt-90) cc_final: 0.7669 (ptt-90) REVERT: A 1057 GLU cc_start: 0.7661 (tt0) cc_final: 0.7439 (tt0) REVERT: A 1131 LYS cc_start: 0.8620 (tttp) cc_final: 0.8305 (ttmm) REVERT: A 1196 GLU cc_start: 0.7555 (tt0) cc_final: 0.7247 (tp30) REVERT: A 1264 MET cc_start: 0.4736 (tpt) cc_final: 0.2783 (pmt) REVERT: B 72 ASN cc_start: 0.6802 (t0) cc_final: 0.6279 (t0) REVERT: B 74 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7048 (mmtp) REVERT: B 81 SER cc_start: 0.7838 (m) cc_final: 0.7601 (p) REVERT: B 205 TYR cc_start: 0.6571 (m-80) cc_final: 0.6166 (m-80) REVERT: B 657 GLN cc_start: 0.7590 (mm110) cc_final: 0.7325 (mm110) REVERT: B 860 GLU cc_start: 0.6379 (mm-30) cc_final: 0.5850 (mp0) REVERT: B 967 GLN cc_start: 0.6724 (tp40) cc_final: 0.6428 (tp40) REVERT: B 1055 GLU cc_start: 0.7122 (tt0) cc_final: 0.6820 (tt0) REVERT: B 1151 LYS cc_start: 0.8396 (pttp) cc_final: 0.7671 (mmtp) REVERT: C 8 ASN cc_start: 0.8281 (m-40) cc_final: 0.7840 (m-40) REVERT: C 28 ASN cc_start: 0.8401 (t0) cc_final: 0.8146 (t0) REVERT: C 297 LYS cc_start: 0.8231 (tttt) cc_final: 0.8003 (ttpt) REVERT: F 135 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7680 (mt-10) REVERT: I 56 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7503 (tpp80) REVERT: I 126 LYS cc_start: 0.5867 (mmtt) cc_final: 0.5498 (tppt) REVERT: I 166 PHE cc_start: 0.8307 (t80) cc_final: 0.8013 (t80) REVERT: I 177 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7473 (ptmt) REVERT: I 245 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6778 (tmtt) REVERT: I 428 MET cc_start: 0.5957 (mmm) cc_final: 0.5706 (mmm) REVERT: I 636 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6181 (tp30) REVERT: I 643 LYS cc_start: 0.7396 (tppp) cc_final: 0.7156 (tmtt) REVERT: I 713 ASP cc_start: 0.6926 (p0) cc_final: 0.6665 (p0) REVERT: I 715 MET cc_start: 0.7929 (mmp) cc_final: 0.7682 (mmm) REVERT: J 51 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7257 (mt0) REVERT: K 163 VAL cc_start: 0.8081 (m) cc_final: 0.7468 (p) REVERT: K 315 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7619 (mmtm) REVERT: S 135 ASN cc_start: 0.8146 (t0) cc_final: 0.7713 (t0) REVERT: W 410 ASP cc_start: 0.7008 (m-30) cc_final: 0.6801 (m-30) REVERT: W 577 ASP cc_start: 0.6869 (m-30) cc_final: 0.6361 (m-30) outliers start: 20 outliers final: 8 residues processed: 1083 average time/residue: 1.4834 time to fit residues: 1996.6056 Evaluate side-chains 687 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 679 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 356 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 453 optimal weight: 4.9990 chunk 407 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 420 optimal weight: 9.9990 chunk 162 optimal weight: 30.0000 chunk 255 optimal weight: 8.9990 chunk 313 optimal weight: 8.9990 chunk 487 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 343 ASN A 459 GLN A1006 ASN A1140 ASN A1199 ASN A1226 HIS B 282 ASN B 295 HIS B 371 HIS B 376 ASN B 736 ASN B 971 GLN C 24 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 170 ASN I 374 ASN I 448 GLN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 ASN K 203 ASN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 ASN K 547 ASN K 615 GLN K 692 ASN S 58 ASN W 113 ASN W 285 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 46261 Z= 0.343 Angle : 0.598 10.332 62907 Z= 0.323 Chirality : 0.047 0.173 7140 Planarity : 0.004 0.043 7663 Dihedral : 13.380 177.815 6787 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.98 % Allowed : 10.51 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.54 (0.12), residues: 5306 helix: 1.59 (0.12), residues: 1955 sheet: -0.30 (0.18), residues: 780 loop : -0.34 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 235 HIS 0.012 0.001 HIS B 295 PHE 0.039 0.002 PHE A 938 TYR 0.026 0.002 TYR W 605 ARG 0.008 0.001 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 690 time to evaluate : 5.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.6861 (p0) REVERT: A 56 GLU cc_start: 0.7823 (pt0) cc_final: 0.7118 (tt0) REVERT: A 71 THR cc_start: 0.8812 (m) cc_final: 0.8320 (t) REVERT: A 137 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8357 (mp10) REVERT: A 327 GLN cc_start: 0.7889 (tm130) cc_final: 0.7604 (tm-30) REVERT: A 520 ASP cc_start: 0.7809 (m-30) cc_final: 0.7600 (m-30) REVERT: A 522 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7781 (mt-10) REVERT: A 592 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5859 (mm-30) REVERT: A 604 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6843 (mm-30) REVERT: A 608 LYS cc_start: 0.6640 (mptt) cc_final: 0.6260 (tttt) REVERT: A 617 LYS cc_start: 0.8164 (mttt) cc_final: 0.7767 (tttt) REVERT: A 650 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6420 (mtm110) REVERT: A 675 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 694 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6711 (pp20) REVERT: A 863 MET cc_start: 0.8713 (ttm) cc_final: 0.8435 (ttm) REVERT: A 1042 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7715 (mt-10) REVERT: A 1126 GLU cc_start: 0.7692 (tt0) cc_final: 0.7284 (tm-30) REVERT: A 1131 LYS cc_start: 0.8636 (tttp) cc_final: 0.8413 (ttmm) REVERT: A 1196 GLU cc_start: 0.7679 (tt0) cc_final: 0.7294 (tm-30) REVERT: A 1264 MET cc_start: 0.5104 (tpt) cc_final: 0.3302 (pmt) REVERT: B 64 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7238 (pp20) REVERT: B 72 ASN cc_start: 0.6675 (t0) cc_final: 0.6016 (t0) REVERT: B 74 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7244 (mmtm) REVERT: B 173 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7764 (mttp) REVERT: B 386 MET cc_start: 0.6466 (mmm) cc_final: 0.5830 (mmm) REVERT: B 413 SER cc_start: 0.7847 (OUTLIER) cc_final: 0.7507 (t) REVERT: B 654 GLU cc_start: 0.7425 (pt0) cc_final: 0.6840 (tp30) REVERT: B 657 GLN cc_start: 0.7718 (mm110) cc_final: 0.7403 (mm110) REVERT: B 823 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6556 (tp) REVERT: B 860 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6026 (mp0) REVERT: B 887 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 890 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8379 (ptpp) REVERT: B 923 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7700 (mtt-85) REVERT: B 967 GLN cc_start: 0.6952 (tp40) cc_final: 0.6654 (tp40) REVERT: B 1151 LYS cc_start: 0.8502 (pttp) cc_final: 0.7793 (mmtp) REVERT: C 90 ARG cc_start: 0.7407 (mtm110) cc_final: 0.6981 (mtm110) REVERT: F 135 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7911 (mt-10) REVERT: G 22 ASP cc_start: 0.8308 (m-30) cc_final: 0.8071 (m-30) REVERT: G 92 GLU cc_start: 0.5896 (pm20) cc_final: 0.5394 (pm20) REVERT: I 56 ARG cc_start: 0.8414 (ttm170) cc_final: 0.7492 (tpp80) REVERT: I 107 MET cc_start: 0.7794 (tpt) cc_final: 0.7562 (tpp) REVERT: I 176 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7215 (tm-30) REVERT: I 177 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7539 (ptmt) REVERT: I 180 ASP cc_start: 0.7692 (p0) cc_final: 0.7382 (m-30) REVERT: I 245 LYS cc_start: 0.7347 (ttpt) cc_final: 0.6741 (tmtt) REVERT: I 636 GLU cc_start: 0.6457 (mm-30) cc_final: 0.6182 (tp30) REVERT: I 715 MET cc_start: 0.8015 (mmp) cc_final: 0.7746 (mmm) REVERT: J 25 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8357 (mptt) REVERT: J 52 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8231 (mpt-90) REVERT: K 315 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7876 (mmtt) REVERT: K 392 MET cc_start: 0.7768 (tpp) cc_final: 0.6922 (tpt) REVERT: K 573 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: S 135 ASN cc_start: 0.8082 (t0) cc_final: 0.7839 (t0) REVERT: W 198 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8046 (mtmm) REVERT: W 313 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6738 (p) REVERT: W 315 TYR cc_start: 0.6651 (m-80) cc_final: 0.6427 (m-80) REVERT: W 577 ASP cc_start: 0.6943 (m-30) cc_final: 0.6675 (m-30) outliers start: 147 outliers final: 63 residues processed: 783 average time/residue: 1.5194 time to fit residues: 1479.8764 Evaluate side-chains 695 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 620 time to evaluate : 5.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain I residue 170 ASN Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 677 ILE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 435 HIS Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 562 THR Chi-restraints excluded: chain W residue 583 ASP Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 271 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 405 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 488 optimal weight: 5.9990 chunk 527 optimal weight: 0.0980 chunk 435 optimal weight: 2.9990 chunk 484 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 391 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN A1226 HIS B 282 ASN B 295 HIS B 371 HIS C 8 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS G 37 HIS I 170 ASN I 254 ASN J 57 GLN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 ASN S 55 ASN S 58 ASN W 372 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46261 Z= 0.207 Angle : 0.521 9.382 62907 Z= 0.281 Chirality : 0.043 0.166 7140 Planarity : 0.003 0.040 7663 Dihedral : 13.488 179.536 6777 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.81 % Allowed : 12.05 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 5306 helix: 1.54 (0.12), residues: 1973 sheet: -0.23 (0.19), residues: 768 loop : -0.35 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 365 HIS 0.009 0.001 HIS B 295 PHE 0.031 0.001 PHE A 938 TYR 0.018 0.001 TYR W 605 ARG 0.005 0.000 ARG A1010 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 670 time to evaluate : 5.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.6799 (p0) REVERT: A 56 GLU cc_start: 0.7858 (pt0) cc_final: 0.7041 (tt0) REVERT: A 114 HIS cc_start: 0.6975 (m-70) cc_final: 0.6695 (p-80) REVERT: A 136 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7521 (mpp) REVERT: A 137 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8337 (mp10) REVERT: A 327 GLN cc_start: 0.7929 (tm130) cc_final: 0.7635 (tm-30) REVERT: A 420 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 520 ASP cc_start: 0.7821 (m-30) cc_final: 0.7610 (m-30) REVERT: A 522 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 604 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6850 (mm-30) REVERT: A 608 LYS cc_start: 0.6663 (mptt) cc_final: 0.6273 (tttt) REVERT: A 617 LYS cc_start: 0.8115 (mttt) cc_final: 0.7875 (mttp) REVERT: A 650 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6442 (mtm110) REVERT: A 675 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 694 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6683 (pp20) REVERT: A 963 GLU cc_start: 0.7525 (tp30) cc_final: 0.7233 (tp30) REVERT: A 1042 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7703 (mt-10) REVERT: A 1126 GLU cc_start: 0.7660 (tt0) cc_final: 0.7228 (tm-30) REVERT: A 1264 MET cc_start: 0.5191 (tpt) cc_final: 0.3247 (pmt) REVERT: B 74 LYS cc_start: 0.7751 (mtpt) cc_final: 0.7286 (mmtm) REVERT: B 173 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7746 (mttp) REVERT: B 386 MET cc_start: 0.6559 (mmm) cc_final: 0.6067 (mmm) REVERT: B 413 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7330 (t) REVERT: B 654 GLU cc_start: 0.7494 (pt0) cc_final: 0.6933 (tp30) REVERT: B 657 GLN cc_start: 0.7734 (mm110) cc_final: 0.7494 (mm110) REVERT: B 860 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6063 (mp0) REVERT: B 887 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 890 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8447 (ptpp) REVERT: B 923 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7722 (mtt-85) REVERT: B 967 GLN cc_start: 0.6925 (tp40) cc_final: 0.6678 (tp40) REVERT: B 1036 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6319 (tmtm) REVERT: B 1151 LYS cc_start: 0.8544 (pttp) cc_final: 0.7840 (mmtp) REVERT: C 15 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: C 90 ARG cc_start: 0.7415 (mtm110) cc_final: 0.7012 (mtm110) REVERT: C 115 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: F 131 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: F 135 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7979 (mt-10) REVERT: G 22 ASP cc_start: 0.8342 (m-30) cc_final: 0.8079 (m-30) REVERT: G 92 GLU cc_start: 0.5845 (pm20) cc_final: 0.5321 (pm20) REVERT: I 56 ARG cc_start: 0.8408 (ttm170) cc_final: 0.7517 (tpp80) REVERT: I 107 MET cc_start: 0.7731 (tpt) cc_final: 0.7471 (tpp) REVERT: I 121 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7854 (tpp) REVERT: I 176 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7234 (tm-30) REVERT: I 180 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: I 194 LEU cc_start: 0.7759 (mt) cc_final: 0.7494 (mm) REVERT: I 245 LYS cc_start: 0.7335 (ttpt) cc_final: 0.6734 (tmtt) REVERT: I 636 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6154 (tp30) REVERT: I 715 MET cc_start: 0.8024 (mmp) cc_final: 0.7778 (mmm) REVERT: J 25 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8535 (mptt) REVERT: K 145 SER cc_start: 0.6980 (m) cc_final: 0.6733 (m) REVERT: S 60 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7235 (mtmt) REVERT: W 198 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7920 (mtmm) REVERT: W 313 VAL cc_start: 0.7205 (OUTLIER) cc_final: 0.6625 (p) REVERT: W 393 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6175 (pp-130) outliers start: 139 outliers final: 69 residues processed: 756 average time/residue: 1.5063 time to fit residues: 1420.0278 Evaluate side-chains 719 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 634 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 791 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 388 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 278 VAL Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Chi-restraints excluded: chain W residue 610 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 482 optimal weight: 5.9990 chunk 367 optimal weight: 30.0000 chunk 253 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 490 optimal weight: 8.9990 chunk 519 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 464 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 295 HIS B 371 HIS B 971 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 355 GLN K 615 GLN S 55 ASN S 58 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 372 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 46261 Z= 0.374 Angle : 0.597 10.539 62907 Z= 0.321 Chirality : 0.046 0.196 7140 Planarity : 0.004 0.045 7663 Dihedral : 13.865 179.516 6777 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.87 % Allowed : 12.05 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.22 (0.11), residues: 5306 helix: 1.26 (0.12), residues: 1975 sheet: -0.43 (0.18), residues: 781 loop : -0.48 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 43 HIS 0.010 0.001 HIS B 295 PHE 0.035 0.002 PHE A 938 TYR 0.022 0.002 TYR K 278 ARG 0.006 0.001 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 655 time to evaluate : 5.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7335 (p0) REVERT: A 136 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7511 (mpp) REVERT: A 327 GLN cc_start: 0.7895 (tm130) cc_final: 0.7611 (tm-30) REVERT: A 488 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.7828 (ttm110) REVERT: A 522 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 604 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6784 (mm-30) REVERT: A 608 LYS cc_start: 0.6764 (mptt) cc_final: 0.6232 (tttt) REVERT: A 617 LYS cc_start: 0.8165 (mttt) cc_final: 0.7657 (tttt) REVERT: A 650 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6130 (ttp80) REVERT: A 675 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7935 (mm-30) REVERT: A 694 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: A 963 GLU cc_start: 0.7581 (tp30) cc_final: 0.7335 (tp30) REVERT: A 1126 GLU cc_start: 0.7683 (tt0) cc_final: 0.7244 (tm-30) REVERT: A 1264 MET cc_start: 0.5430 (tpt) cc_final: 0.3263 (pmt) REVERT: B 74 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7468 (mmtm) REVERT: B 173 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7741 (mttp) REVERT: B 386 MET cc_start: 0.6491 (mmm) cc_final: 0.6043 (mmm) REVERT: B 413 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7198 (t) REVERT: B 860 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6088 (mp0) REVERT: B 890 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8419 (ptpp) REVERT: B 923 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7899 (mtt-85) REVERT: B 1036 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6723 (tmtm) REVERT: B 1151 LYS cc_start: 0.8515 (pttp) cc_final: 0.7760 (mmtp) REVERT: C 15 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: C 90 ARG cc_start: 0.7465 (mtm110) cc_final: 0.7057 (mtm110) REVERT: E 21 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6996 (ttm-80) REVERT: F 131 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: F 135 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8009 (mt-10) REVERT: G 18 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: G 92 GLU cc_start: 0.5729 (pm20) cc_final: 0.5112 (pm20) REVERT: I 107 MET cc_start: 0.7811 (tpt) cc_final: 0.7572 (tpp) REVERT: I 121 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7920 (tpp) REVERT: I 126 LYS cc_start: 0.5551 (tppt) cc_final: 0.5244 (tppt) REVERT: I 176 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7346 (tm-30) REVERT: I 180 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: I 194 LEU cc_start: 0.7809 (mt) cc_final: 0.7537 (mm) REVERT: I 245 LYS cc_start: 0.7272 (ttpt) cc_final: 0.6711 (tmtt) REVERT: I 304 LEU cc_start: 0.7142 (mt) cc_final: 0.6923 (mm) REVERT: I 539 ARG cc_start: 0.4679 (mmp80) cc_final: 0.4183 (ttm170) REVERT: I 632 THR cc_start: 0.8376 (p) cc_final: 0.8161 (p) REVERT: I 636 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6199 (tp30) REVERT: I 715 MET cc_start: 0.7994 (mmp) cc_final: 0.7720 (mmm) REVERT: I 770 LYS cc_start: 0.8141 (ptmt) cc_final: 0.7894 (ptmt) REVERT: J 51 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: J 52 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8192 (mpt-90) REVERT: K 540 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7298 (tm-30) REVERT: K 544 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6320 (mt-10) REVERT: K 559 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: K 573 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: S 60 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7179 (mtmt) REVERT: W 198 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: W 393 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6270 (pp-130) REVERT: W 463 ASP cc_start: 0.6847 (t0) cc_final: 0.6633 (t0) outliers start: 191 outliers final: 90 residues processed: 774 average time/residue: 1.5441 time to fit residues: 1479.3579 Evaluate side-chains 733 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 624 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 662 ASP Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 559 MET Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 278 VAL Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 435 HIS Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 562 THR Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 432 optimal weight: 0.7980 chunk 294 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 386 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 442 optimal weight: 4.9990 chunk 358 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 265 optimal weight: 9.9990 chunk 465 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 282 ASN B 295 HIS B 371 HIS B 967 GLN B 971 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 ASN S 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 46261 Z= 0.271 Angle : 0.557 10.615 62907 Z= 0.299 Chirality : 0.044 0.187 7140 Planarity : 0.004 0.043 7663 Dihedral : 13.873 179.642 6777 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.36 % Allowed : 13.41 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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 (0.12), residues: 5306 helix: 1.29 (0.12), residues: 1968 sheet: -0.37 (0.18), residues: 770 loop : -0.49 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 365 HIS 0.011 0.001 HIS B 295 PHE 0.033 0.002 PHE A 938 TYR 0.019 0.002 TYR K 211 ARG 0.005 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 644 time to evaluate : 5.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7269 (p0) REVERT: A 136 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7602 (mpp) REVERT: A 137 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8088 (mp10) REVERT: A 327 GLN cc_start: 0.7894 (tm130) cc_final: 0.7635 (tm-30) REVERT: A 522 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 604 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6791 (mm-30) REVERT: A 608 LYS cc_start: 0.6691 (mptt) cc_final: 0.6196 (tttt) REVERT: A 617 LYS cc_start: 0.8184 (mttt) cc_final: 0.7952 (mttp) REVERT: A 650 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6124 (ttp80) REVERT: A 675 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 694 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6667 (pp20) REVERT: A 963 GLU cc_start: 0.7558 (tp30) cc_final: 0.7300 (tp30) REVERT: A 1126 GLU cc_start: 0.7702 (tt0) cc_final: 0.7261 (tm-30) REVERT: A 1131 LYS cc_start: 0.8545 (tttp) cc_final: 0.8285 (ttmm) REVERT: A 1264 MET cc_start: 0.5341 (tpt) cc_final: 0.3305 (pmt) REVERT: B 74 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7422 (mmtm) REVERT: B 120 TYR cc_start: 0.6452 (t80) cc_final: 0.6223 (t80) REVERT: B 173 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7773 (mttp) REVERT: B 386 MET cc_start: 0.6483 (mmm) cc_final: 0.6021 (mmm) REVERT: B 413 SER cc_start: 0.7632 (OUTLIER) cc_final: 0.7202 (t) REVERT: B 720 ARG cc_start: 0.7936 (ptm-80) cc_final: 0.7507 (ptm-80) REVERT: B 860 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6174 (mp0) REVERT: B 890 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8433 (ptpp) REVERT: B 923 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7879 (mtt-85) REVERT: B 1036 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6773 (tmtm) REVERT: B 1151 LYS cc_start: 0.8517 (pttp) cc_final: 0.7776 (mmtp) REVERT: C 15 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: E 21 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6950 (ttm-80) REVERT: F 131 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: F 135 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8042 (mt-10) REVERT: G 55 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: G 92 GLU cc_start: 0.5746 (pm20) cc_final: 0.5213 (pm20) REVERT: G 149 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: I 107 MET cc_start: 0.7772 (tpt) cc_final: 0.7471 (tpp) REVERT: I 121 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7971 (tpp) REVERT: I 126 LYS cc_start: 0.5469 (tppt) cc_final: 0.5172 (tppt) REVERT: I 176 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7330 (tm-30) REVERT: I 180 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: I 194 LEU cc_start: 0.7861 (mt) cc_final: 0.7606 (mm) REVERT: I 245 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6710 (tmtt) REVERT: I 304 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6895 (mm) REVERT: I 338 VAL cc_start: 0.5084 (OUTLIER) cc_final: 0.4854 (t) REVERT: I 539 ARG cc_start: 0.4698 (mmp80) cc_final: 0.4245 (ttm170) REVERT: I 636 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6178 (tp30) REVERT: I 715 MET cc_start: 0.7996 (mmp) cc_final: 0.7738 (mmm) REVERT: I 770 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7898 (ptmt) REVERT: J 51 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: J 52 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8115 (mpt-90) REVERT: K 161 MET cc_start: 0.7866 (mmp) cc_final: 0.7649 (mmm) REVERT: K 573 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8441 (mt0) REVERT: S 60 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7121 (mtmt) REVERT: W 198 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8051 (mtmm) REVERT: W 393 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6174 (pp-130) REVERT: W 463 ASP cc_start: 0.6795 (t0) cc_final: 0.6559 (t0) outliers start: 166 outliers final: 84 residues processed: 747 average time/residue: 1.5465 time to fit residues: 1434.0858 Evaluate side-chains 721 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 616 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 662 ASP Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 322 LEU Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 523 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 174 optimal weight: 0.0870 chunk 467 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 519 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 343 ASN A1222 ASN B 295 HIS B 371 HIS B 376 ASN B 967 GLN B 971 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 703 ASN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 GLN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46261 Z= 0.254 Angle : 0.550 11.692 62907 Z= 0.295 Chirality : 0.044 0.178 7140 Planarity : 0.004 0.042 7663 Dihedral : 13.891 179.854 6777 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.40 % Allowed : 13.89 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.27 (0.12), residues: 5306 helix: 1.31 (0.12), residues: 1973 sheet: -0.34 (0.18), residues: 771 loop : -0.50 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 365 HIS 0.011 0.001 HIS B 295 PHE 0.032 0.001 PHE A 938 TYR 0.016 0.001 TYR W 368 ARG 0.009 0.000 ARG A1010 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 638 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7255 (p0) REVERT: A 136 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7627 (mpp) REVERT: A 137 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8039 (mp10) REVERT: A 327 GLN cc_start: 0.7908 (tm130) cc_final: 0.7588 (tm-30) REVERT: A 522 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 604 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 617 LYS cc_start: 0.8174 (mttt) cc_final: 0.7727 (tttt) REVERT: A 650 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6182 (ttp80) REVERT: A 675 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 694 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6629 (pp20) REVERT: A 963 GLU cc_start: 0.7553 (tp30) cc_final: 0.7282 (tp30) REVERT: A 1010 ARG cc_start: 0.8367 (ptt90) cc_final: 0.8024 (ptt-90) REVERT: A 1126 GLU cc_start: 0.7727 (tt0) cc_final: 0.7282 (tm-30) REVERT: A 1131 LYS cc_start: 0.8565 (tttp) cc_final: 0.8312 (ttmm) REVERT: A 1264 MET cc_start: 0.5528 (tpt) cc_final: 0.3337 (pmt) REVERT: B 74 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7414 (mmtm) REVERT: B 120 TYR cc_start: 0.6473 (t80) cc_final: 0.6224 (t80) REVERT: B 173 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7798 (mttt) REVERT: B 190 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7078 (t80) REVERT: B 206 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7371 (mmm-85) REVERT: B 386 MET cc_start: 0.6523 (mmm) cc_final: 0.6058 (mmm) REVERT: B 413 SER cc_start: 0.7691 (OUTLIER) cc_final: 0.7252 (t) REVERT: B 720 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7532 (ptm-80) REVERT: B 860 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6186 (mp0) REVERT: B 890 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8396 (ptpp) REVERT: B 923 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7866 (mtt-85) REVERT: B 1036 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6721 (tmtm) REVERT: B 1151 LYS cc_start: 0.8530 (pttp) cc_final: 0.7808 (mmtp) REVERT: C 15 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: E 3 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: E 21 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6950 (ttm-80) REVERT: F 131 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: G 18 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: G 55 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: G 92 GLU cc_start: 0.5714 (pm20) cc_final: 0.5146 (pm20) REVERT: G 149 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5811 (mp0) REVERT: I 107 MET cc_start: 0.7767 (tpt) cc_final: 0.7493 (tpp) REVERT: I 126 LYS cc_start: 0.5426 (tppt) cc_final: 0.5127 (tppt) REVERT: I 177 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7440 (tttt) REVERT: I 180 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: I 194 LEU cc_start: 0.7856 (mt) cc_final: 0.7649 (mm) REVERT: I 245 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6781 (tmtt) REVERT: I 304 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6971 (mm) REVERT: I 338 VAL cc_start: 0.5115 (OUTLIER) cc_final: 0.4883 (t) REVERT: I 487 MET cc_start: 0.4456 (mmm) cc_final: 0.4003 (pmt) REVERT: I 539 ARG cc_start: 0.4718 (mmp80) cc_final: 0.4259 (ttm170) REVERT: I 576 ARG cc_start: 0.6918 (ptm160) cc_final: 0.6700 (ptm-80) REVERT: I 636 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6224 (tp30) REVERT: I 770 LYS cc_start: 0.8038 (ptmt) cc_final: 0.7793 (ptmt) REVERT: J 51 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: J 52 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8087 (mpt-90) REVERT: K 315 LYS cc_start: 0.8509 (mmtm) cc_final: 0.7993 (mmtt) REVERT: S 60 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7088 (mtmt) REVERT: S 81 ASP cc_start: 0.8120 (p0) cc_final: 0.7919 (p0) REVERT: W 198 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8051 (mtmm) REVERT: W 393 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6130 (pp-130) REVERT: W 409 ASN cc_start: 0.6892 (t0) cc_final: 0.6646 (t0) REVERT: W 454 ARG cc_start: 0.6632 (mmt90) cc_final: 0.6405 (mmt90) REVERT: W 463 ASP cc_start: 0.6751 (t0) cc_final: 0.6526 (t0) outliers start: 168 outliers final: 86 residues processed: 749 average time/residue: 1.5469 time to fit residues: 1438.4223 Evaluate side-chains 728 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 620 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain B residue 1055 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 278 VAL Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 500 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 296 optimal weight: 8.9990 chunk 379 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 437 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 chunk 517 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 282 ASN B 295 HIS B 371 HIS B 376 ASN B 967 GLN B 971 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 632 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 46261 Z= 0.313 Angle : 0.580 12.485 62907 Z= 0.310 Chirality : 0.045 0.219 7140 Planarity : 0.004 0.042 7663 Dihedral : 13.973 179.923 6777 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.16 % Allowed : 14.64 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.16 (0.11), residues: 5306 helix: 1.18 (0.12), residues: 1980 sheet: -0.36 (0.18), residues: 774 loop : -0.55 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 365 HIS 0.012 0.001 HIS B 295 PHE 0.033 0.002 PHE A 938 TYR 0.020 0.002 TYR K 211 ARG 0.007 0.000 ARG A1010 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 629 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7401 (p0) REVERT: A 136 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7558 (mpp) REVERT: A 327 GLN cc_start: 0.7911 (tm130) cc_final: 0.7650 (tm-30) REVERT: A 488 ARG cc_start: 0.8312 (ttp-110) cc_final: 0.7825 (ttm110) REVERT: A 522 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 604 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6792 (mm-30) REVERT: A 617 LYS cc_start: 0.8177 (mttt) cc_final: 0.7758 (tttt) REVERT: A 650 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6215 (ttp80) REVERT: A 675 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7983 (mm-30) REVERT: A 694 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: A 766 MET cc_start: 0.8599 (ttm) cc_final: 0.8359 (ttp) REVERT: A 963 GLU cc_start: 0.7558 (tp30) cc_final: 0.7271 (tp30) REVERT: A 1010 ARG cc_start: 0.8349 (ptt90) cc_final: 0.8022 (ptt-90) REVERT: A 1126 GLU cc_start: 0.7750 (tt0) cc_final: 0.7259 (tm-30) REVERT: A 1131 LYS cc_start: 0.8587 (tttp) cc_final: 0.8326 (ttmm) REVERT: A 1264 MET cc_start: 0.5585 (tpt) cc_final: 0.3361 (pmt) REVERT: B 74 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7410 (mmtm) REVERT: B 120 TYR cc_start: 0.6499 (t80) cc_final: 0.6277 (t80) REVERT: B 173 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7783 (mttp) REVERT: B 190 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7092 (t80) REVERT: B 206 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7371 (mmm-85) REVERT: B 386 MET cc_start: 0.6546 (mmm) cc_final: 0.6152 (mmm) REVERT: B 413 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7264 (t) REVERT: B 860 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6187 (mp0) REVERT: B 890 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8403 (ptpp) REVERT: B 923 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7903 (mtt-85) REVERT: B 946 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8375 (mtmt) REVERT: B 967 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6457 (mm110) REVERT: B 1036 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6692 (tmtm) REVERT: B 1151 LYS cc_start: 0.8527 (pttp) cc_final: 0.7791 (mmtp) REVERT: C 15 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: E 3 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: E 21 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7046 (ttm-80) REVERT: F 131 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: F 135 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8082 (mt-10) REVERT: G 18 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: G 55 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: G 92 GLU cc_start: 0.5689 (pm20) cc_final: 0.5127 (pm20) REVERT: G 149 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5924 (mp0) REVERT: I 107 MET cc_start: 0.7779 (tpt) cc_final: 0.7569 (tpp) REVERT: I 126 LYS cc_start: 0.5436 (tppt) cc_final: 0.5130 (tppt) REVERT: I 177 LYS cc_start: 0.7822 (mtmt) cc_final: 0.7426 (tttt) REVERT: I 180 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: I 194 LEU cc_start: 0.7848 (mt) cc_final: 0.7631 (mm) REVERT: I 245 LYS cc_start: 0.7278 (ttpt) cc_final: 0.6787 (tmtt) REVERT: I 304 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.7005 (mm) REVERT: I 338 VAL cc_start: 0.5110 (OUTLIER) cc_final: 0.4883 (t) REVERT: I 487 MET cc_start: 0.4452 (mmm) cc_final: 0.3992 (pmt) REVERT: I 539 ARG cc_start: 0.4724 (mmp80) cc_final: 0.4218 (ttm170) REVERT: I 576 ARG cc_start: 0.6927 (ptm160) cc_final: 0.6671 (ptm-80) REVERT: I 636 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6228 (tp30) REVERT: I 770 LYS cc_start: 0.8031 (ptmt) cc_final: 0.7810 (ptmt) REVERT: J 24 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7651 (mtm180) REVERT: J 51 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: J 52 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8106 (mpt-90) REVERT: K 559 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8185 (ttp) REVERT: S 60 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7057 (mtmt) REVERT: W 47 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7287 (ttt) REVERT: W 198 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8137 (mtmm) REVERT: W 393 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6240 (pp-130) REVERT: W 463 ASP cc_start: 0.6824 (t0) cc_final: 0.6598 (t0) REVERT: W 556 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7766 (ttp-170) outliers start: 156 outliers final: 90 residues processed: 727 average time/residue: 1.5723 time to fit residues: 1413.8553 Evaluate side-chains 730 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 613 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 967 GLN Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 662 ASP Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 ASN Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 559 MET Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 47 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 295 LEU Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 435 HIS Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 320 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 329 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 255 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 406 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 159 ASN B 295 HIS B 371 HIS B 376 ASN B 391 ASN B 967 GLN B 971 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN G 100 GLN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 GLN K 281 HIS K 692 ASN S 55 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 46261 Z= 0.369 Angle : 0.606 12.931 62907 Z= 0.323 Chirality : 0.046 0.182 7140 Planarity : 0.004 0.044 7663 Dihedral : 14.027 179.998 6777 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.30 % Allowed : 14.82 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.07 (0.11), residues: 5306 helix: 1.10 (0.12), residues: 1969 sheet: -0.41 (0.18), residues: 781 loop : -0.58 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 365 HIS 0.012 0.001 HIS B 295 PHE 0.035 0.002 PHE A 938 TYR 0.022 0.002 TYR S 78 ARG 0.006 0.001 ARG A1010 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 622 time to evaluate : 5.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7424 (p0) REVERT: A 136 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: A 327 GLN cc_start: 0.7885 (tm130) cc_final: 0.7592 (tm-30) REVERT: A 488 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7853 (ttm110) REVERT: A 604 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6792 (mm-30) REVERT: A 608 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6534 (ttmm) REVERT: A 617 LYS cc_start: 0.8185 (mttt) cc_final: 0.7777 (tttt) REVERT: A 650 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6232 (ttp80) REVERT: A 675 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 694 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6695 (pp20) REVERT: A 766 MET cc_start: 0.8598 (ttm) cc_final: 0.8369 (ttp) REVERT: A 963 GLU cc_start: 0.7559 (tp30) cc_final: 0.7273 (tp30) REVERT: A 1010 ARG cc_start: 0.8351 (ptt90) cc_final: 0.8026 (ptt-90) REVERT: A 1126 GLU cc_start: 0.7755 (tt0) cc_final: 0.7280 (tm-30) REVERT: A 1131 LYS cc_start: 0.8627 (tttp) cc_final: 0.8354 (ttmm) REVERT: A 1264 MET cc_start: 0.5651 (tpt) cc_final: 0.3390 (pmt) REVERT: B 74 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7392 (mmtm) REVERT: B 120 TYR cc_start: 0.6506 (t80) cc_final: 0.6276 (t80) REVERT: B 173 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7781 (mttp) REVERT: B 190 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7090 (t80) REVERT: B 206 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7343 (mmm-85) REVERT: B 386 MET cc_start: 0.6559 (mmm) cc_final: 0.6159 (mmm) REVERT: B 413 SER cc_start: 0.7666 (OUTLIER) cc_final: 0.7195 (t) REVERT: B 544 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7542 (ptm) REVERT: B 890 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8416 (ptpp) REVERT: B 923 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7935 (mtt-85) REVERT: B 946 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8336 (mtmt) REVERT: B 967 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6503 (mm110) REVERT: B 1036 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6752 (tmtm) REVERT: B 1151 LYS cc_start: 0.8534 (pttp) cc_final: 0.7746 (mttt) REVERT: C 15 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: E 3 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: E 21 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6900 (ttm-80) REVERT: E 55 ASP cc_start: 0.8007 (t70) cc_final: 0.7782 (t0) REVERT: F 131 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: F 135 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8013 (mt-10) REVERT: G 18 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: G 55 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: G 92 GLU cc_start: 0.5686 (pm20) cc_final: 0.5100 (pm20) REVERT: G 149 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: I 107 MET cc_start: 0.7784 (tpt) cc_final: 0.7566 (tpp) REVERT: I 126 LYS cc_start: 0.5437 (tppt) cc_final: 0.5133 (tppt) REVERT: I 176 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7511 (tm-30) REVERT: I 177 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7446 (tttt) REVERT: I 180 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: I 194 LEU cc_start: 0.7814 (mt) cc_final: 0.7593 (mm) REVERT: I 245 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6738 (tmtt) REVERT: I 304 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7052 (mm) REVERT: I 338 VAL cc_start: 0.5019 (OUTLIER) cc_final: 0.4789 (t) REVERT: I 487 MET cc_start: 0.4432 (mmm) cc_final: 0.3975 (pmt) REVERT: I 539 ARG cc_start: 0.4725 (mmp80) cc_final: 0.4273 (ttm170) REVERT: I 576 ARG cc_start: 0.6962 (ptm160) cc_final: 0.6679 (ptm-80) REVERT: I 636 GLU cc_start: 0.6455 (mm-30) cc_final: 0.6235 (tp30) REVERT: I 770 LYS cc_start: 0.8021 (ptmt) cc_final: 0.7806 (ptmt) REVERT: J 24 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7666 (mtm180) REVERT: J 51 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: J 52 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8144 (mpt-90) REVERT: K 559 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: S 60 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7475 (mtpp) REVERT: W 198 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8091 (mtmm) REVERT: W 393 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6211 (pp-130) REVERT: W 409 ASN cc_start: 0.6975 (t0) cc_final: 0.6742 (t0) REVERT: W 463 ASP cc_start: 0.6868 (t0) cc_final: 0.6652 (t0) REVERT: W 556 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7820 (ttp-170) outliers start: 163 outliers final: 92 residues processed: 724 average time/residue: 1.5532 time to fit residues: 1395.0737 Evaluate side-chains 725 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 605 time to evaluate : 5.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 967 GLN Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 ASN Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 559 MET Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 278 VAL Chi-restraints excluded: chain W residue 285 GLN Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 435 HIS Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 562 THR Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 470 optimal weight: 10.0000 chunk 495 optimal weight: 0.9980 chunk 452 optimal weight: 6.9990 chunk 482 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 378 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 435 optimal weight: 7.9990 chunk 456 optimal weight: 10.0000 chunk 480 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 159 ASN B 295 HIS B 371 HIS B 376 ASN B 971 GLN E 89 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 ASN S 55 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46261 Z= 0.216 Angle : 0.562 13.203 62907 Z= 0.298 Chirality : 0.044 0.170 7140 Planarity : 0.004 0.052 7663 Dihedral : 13.968 179.628 6777 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.59 % Allowed : 15.67 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.23 (0.12), residues: 5306 helix: 1.25 (0.12), residues: 1972 sheet: -0.32 (0.18), residues: 773 loop : -0.51 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.012 0.001 HIS B 295 PHE 0.030 0.001 PHE A 938 TYR 0.022 0.001 TYR S 78 ARG 0.013 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 625 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7221 (p0) REVERT: A 56 GLU cc_start: 0.7860 (pt0) cc_final: 0.7024 (tt0) REVERT: A 136 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7623 (mpp) REVERT: A 137 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7963 (mp10) REVERT: A 327 GLN cc_start: 0.7897 (tm130) cc_final: 0.7573 (tm-30) REVERT: A 488 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7822 (ttm110) REVERT: A 592 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: A 604 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6756 (mm-30) REVERT: A 617 LYS cc_start: 0.8151 (mttt) cc_final: 0.7838 (mttt) REVERT: A 650 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6219 (ttp80) REVERT: A 675 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 694 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6677 (pp20) REVERT: A 963 GLU cc_start: 0.7467 (tp30) cc_final: 0.7190 (tp30) REVERT: A 1010 ARG cc_start: 0.8317 (ptt90) cc_final: 0.8008 (ptt-90) REVERT: A 1126 GLU cc_start: 0.7683 (tt0) cc_final: 0.7275 (tm-30) REVERT: A 1131 LYS cc_start: 0.8594 (tttp) cc_final: 0.8339 (ttmm) REVERT: A 1264 MET cc_start: 0.5625 (tpt) cc_final: 0.3343 (pmt) REVERT: B 74 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7367 (mmtm) REVERT: B 120 TYR cc_start: 0.6421 (t80) cc_final: 0.6145 (t80) REVERT: B 190 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7115 (t80) REVERT: B 206 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.7326 (mmm-85) REVERT: B 292 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6476 (mt-10) REVERT: B 386 MET cc_start: 0.6533 (mmm) cc_final: 0.6134 (mmm) REVERT: B 413 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.7191 (t) REVERT: B 720 ARG cc_start: 0.7916 (ptm-80) cc_final: 0.7537 (ptm-80) REVERT: B 774 THR cc_start: 0.8857 (m) cc_final: 0.8583 (p) REVERT: B 890 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8388 (ptpp) REVERT: B 946 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8347 (mtmt) REVERT: B 1036 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6534 (tmtm) REVERT: B 1151 LYS cc_start: 0.8522 (pttp) cc_final: 0.7724 (mptt) REVERT: C 15 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: E 3 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: E 21 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6959 (ttm-80) REVERT: G 18 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7801 (mt-10) REVERT: G 55 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: G 92 GLU cc_start: 0.5718 (pm20) cc_final: 0.5139 (pm20) REVERT: G 149 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: I 107 MET cc_start: 0.7700 (tpt) cc_final: 0.7421 (tpp) REVERT: I 126 LYS cc_start: 0.5410 (tppt) cc_final: 0.5116 (tppt) REVERT: I 177 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7398 (tttt) REVERT: I 180 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: I 194 LEU cc_start: 0.7804 (mt) cc_final: 0.7596 (mm) REVERT: I 245 LYS cc_start: 0.7316 (ttpt) cc_final: 0.6810 (tmtt) REVERT: I 304 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7109 (mm) REVERT: I 338 VAL cc_start: 0.5050 (OUTLIER) cc_final: 0.4817 (t) REVERT: I 539 ARG cc_start: 0.4680 (mmp80) cc_final: 0.4229 (ttm170) REVERT: I 576 ARG cc_start: 0.6995 (ptm160) cc_final: 0.6720 (ptm-80) REVERT: I 636 GLU cc_start: 0.6402 (mm-30) cc_final: 0.6188 (tp30) REVERT: I 770 LYS cc_start: 0.8029 (ptmt) cc_final: 0.7820 (ptmt) REVERT: J 24 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7631 (mtm180) REVERT: J 51 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: J 52 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8096 (mpt-90) REVERT: S 60 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7457 (mtpp) REVERT: W 198 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: W 393 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6089 (pp-130) REVERT: W 409 ASN cc_start: 0.6754 (t0) cc_final: 0.6542 (t0) REVERT: W 463 ASP cc_start: 0.6779 (t0) cc_final: 0.6574 (t0) outliers start: 128 outliers final: 78 residues processed: 709 average time/residue: 1.6035 time to fit residues: 1405.2552 Evaluate side-chains 710 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 610 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 ASN Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 316 optimal weight: 9.9990 chunk 510 optimal weight: 3.9990 chunk 311 optimal weight: 0.5980 chunk 241 optimal weight: 0.5980 chunk 354 optimal weight: 5.9990 chunk 534 optimal weight: 3.9990 chunk 492 optimal weight: 6.9990 chunk 426 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 159 ASN B 295 HIS B 371 HIS B 376 ASN B 391 ASN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 GLN S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46261 Z= 0.182 Angle : 0.544 14.058 62907 Z= 0.287 Chirality : 0.043 0.171 7140 Planarity : 0.003 0.050 7663 Dihedral : 13.875 179.452 6777 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.25 % Allowed : 16.16 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.39 (0.12), residues: 5306 helix: 1.41 (0.12), residues: 1964 sheet: -0.25 (0.18), residues: 772 loop : -0.43 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 259 HIS 0.012 0.001 HIS B 295 PHE 0.029 0.001 PHE A 938 TYR 0.021 0.001 TYR S 78 ARG 0.012 0.000 ARG C 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 636 time to evaluate : 5.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7186 (p0) REVERT: A 56 GLU cc_start: 0.7886 (pt0) cc_final: 0.7119 (tt0) REVERT: A 136 MET cc_start: 0.7882 (mpt) cc_final: 0.7669 (mpp) REVERT: A 137 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7873 (mp10) REVERT: A 327 GLN cc_start: 0.7931 (tm130) cc_final: 0.7602 (tm-30) REVERT: A 488 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7831 (ttm110) REVERT: A 592 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6333 (tm-30) REVERT: A 604 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6752 (mm-30) REVERT: A 608 LYS cc_start: 0.7167 (ttmm) cc_final: 0.6249 (tttt) REVERT: A 617 LYS cc_start: 0.8121 (mttt) cc_final: 0.7819 (mttt) REVERT: A 650 ARG cc_start: 0.6937 (mtt180) cc_final: 0.6246 (ttp80) REVERT: A 675 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 694 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6586 (pp20) REVERT: A 735 MET cc_start: 0.8392 (mmm) cc_final: 0.8165 (mmm) REVERT: A 963 GLU cc_start: 0.7449 (tp30) cc_final: 0.7184 (tp30) REVERT: A 1010 ARG cc_start: 0.8327 (ptt90) cc_final: 0.8023 (ptt-90) REVERT: A 1126 GLU cc_start: 0.7710 (tt0) cc_final: 0.7276 (tm-30) REVERT: A 1131 LYS cc_start: 0.8567 (tttp) cc_final: 0.8341 (ttmm) REVERT: A 1264 MET cc_start: 0.5361 (tpt) cc_final: 0.3502 (pmt) REVERT: B 59 PHE cc_start: 0.8077 (m-80) cc_final: 0.7864 (m-80) REVERT: B 74 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7357 (mmtm) REVERT: B 120 TYR cc_start: 0.6443 (t80) cc_final: 0.6197 (t80) REVERT: B 173 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7905 (mmmm) REVERT: B 190 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7040 (t80) REVERT: B 206 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7354 (mmm-85) REVERT: B 292 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: B 386 MET cc_start: 0.6541 (mmm) cc_final: 0.6164 (mmm) REVERT: B 413 SER cc_start: 0.7694 (OUTLIER) cc_final: 0.7241 (t) REVERT: B 720 ARG cc_start: 0.7918 (ptm-80) cc_final: 0.7539 (ptm-80) REVERT: B 774 THR cc_start: 0.8824 (m) cc_final: 0.8596 (p) REVERT: B 890 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8434 (ptpp) REVERT: B 946 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8326 (mtmt) REVERT: B 1036 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6525 (tmtm) REVERT: B 1151 LYS cc_start: 0.8527 (pttp) cc_final: 0.7812 (mmtp) REVERT: C 15 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: E 3 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: E 21 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7021 (ttm-80) REVERT: E 55 ASP cc_start: 0.7990 (t70) cc_final: 0.7719 (t0) REVERT: E 179 SER cc_start: 0.8450 (t) cc_final: 0.8195 (t) REVERT: F 131 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: G 18 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7803 (mt-10) REVERT: G 92 GLU cc_start: 0.5659 (pm20) cc_final: 0.5063 (pm20) REVERT: I 107 MET cc_start: 0.7722 (tpt) cc_final: 0.7431 (tpp) REVERT: I 126 LYS cc_start: 0.5404 (tppt) cc_final: 0.5109 (tppt) REVERT: I 177 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7418 (tttt) REVERT: I 180 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: I 245 LYS cc_start: 0.7283 (ttpt) cc_final: 0.6781 (tmtt) REVERT: I 338 VAL cc_start: 0.5176 (OUTLIER) cc_final: 0.4940 (t) REVERT: I 539 ARG cc_start: 0.4709 (mmp80) cc_final: 0.4214 (ttm170) REVERT: I 636 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6123 (tp30) REVERT: I 770 LYS cc_start: 0.8041 (ptmt) cc_final: 0.7827 (ptmt) REVERT: J 24 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7594 (mtm180) REVERT: J 52 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8088 (mpt-90) REVERT: S 60 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7473 (mtpp) REVERT: W 198 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8038 (mtmm) REVERT: W 409 ASN cc_start: 0.6664 (t0) cc_final: 0.6451 (t0) REVERT: W 454 ARG cc_start: 0.6678 (mmt90) cc_final: 0.6397 (mmt90) REVERT: W 463 ASP cc_start: 0.6756 (t0) cc_final: 0.6548 (t0) outliers start: 111 outliers final: 67 residues processed: 710 average time/residue: 1.6116 time to fit residues: 1414.2559 Evaluate side-chains 702 residues out of total 4938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 618 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 ASN Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain K residue 592 ASP Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 338 optimal weight: 20.0000 chunk 453 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 392 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 426 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 438 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A1222 ASN B 295 HIS B 371 HIS B 376 ASN B 967 GLN B 971 GLN F 111 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129182 restraints weight = 66242.754| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.21 r_work: 0.3331 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 46261 Z= 0.306 Angle : 0.596 13.969 62907 Z= 0.315 Chirality : 0.045 0.179 7140 Planarity : 0.004 0.044 7663 Dihedral : 13.989 179.959 6777 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.21 % Allowed : 16.67 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % 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: 0.24 (0.12), residues: 5306 helix: 1.24 (0.12), residues: 1976 sheet: -0.29 (0.18), residues: 764 loop : -0.50 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 259 HIS 0.012 0.001 HIS B 295 PHE 0.033 0.002 PHE A 938 TYR 0.023 0.002 TYR S 78 ARG 0.012 0.000 ARG C 90 =============================================================================== Job complete usr+sys time: 20969.32 seconds wall clock time: 371 minutes 48.95 seconds (22308.95 seconds total)