Starting phenix.real_space_refine on Fri Feb 23 00:59:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6i_0688/02_2024/6j6i_0688_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 218 5.16 5 C 22747 2.51 5 N 6177 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 670": "NH1" <-> "NH2" Residue "C ARG 840": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ARG 391": "NH1" <-> "NH2" Residue "F ARG 492": "NH1" <-> "NH2" Residue "F ARG 513": "NH1" <-> "NH2" Residue "F PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 670": "NH1" <-> "NH2" Residue "F ARG 840": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 211": "NH1" <-> "NH2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G ARG 286": "NH1" <-> "NH2" Residue "G ARG 391": "NH1" <-> "NH2" Residue "G ARG 492": "NH1" <-> "NH2" Residue "G ARG 513": "NH1" <-> "NH2" Residue "G PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 670": "NH1" <-> "NH2" Residue "G ARG 840": "NH1" <-> "NH2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "L ARG 149": "NH1" <-> "NH2" Residue "L ARG 211": "NH1" <-> "NH2" Residue "L ARG 261": "NH1" <-> "NH2" Residue "L ARG 286": "NH1" <-> "NH2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "L ARG 492": "NH1" <-> "NH2" Residue "L ARG 513": "NH1" <-> "NH2" Residue "L PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 670": "NH1" <-> "NH2" Residue "L ARG 840": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "O ARG 149": "NH1" <-> "NH2" Residue "O ARG 211": "NH1" <-> "NH2" Residue "O ARG 261": "NH1" <-> "NH2" Residue "O ARG 286": "NH1" <-> "NH2" Residue "O ARG 391": "NH1" <-> "NH2" Residue "O ARG 492": "NH1" <-> "NH2" Residue "O ARG 513": "NH1" <-> "NH2" Residue "O PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 670": "NH1" <-> "NH2" Residue "O ARG 840": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35992 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1510 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain breaks: 3 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "F" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "G" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "L" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "O" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BQL A 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL A 501 " occ=0.00 Time building chain proxies: 18.63, per 1000 atoms: 0.52 Number of scatterers: 35992 At special positions: 0 Unit cell: (210.563, 173.469, 104.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 218 16.00 P 17 15.00 O 6833 8.00 N 6177 7.00 C 22747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=2, symmetry=0 Simple link: pdb=" C VAL A 252 " - pdb=" N BQL A 501 " Simple link: pdb=" N LYS A 255 " - pdb=" C BQO A 502 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 7.0 seconds 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 163 helices and 31 sheets defined 36.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.737A pdb=" N GLN A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 4.087A pdb=" N LEU A 181 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 275 through 291 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.357A pdb=" N SER B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.727A pdb=" N SER B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 181 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 247 through 263 removed outlier: 4.228A pdb=" N TYR B 252 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'C' and resid 27 through 46 removed outlier: 4.383A pdb=" N LEU C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 56 through 79 removed outlier: 4.125A pdb=" N GLU C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 164 through 179 removed outlier: 3.883A pdb=" N ARG C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C 177 " --> pdb=" O TRP C 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.855A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.583A pdb=" N GLU C 345 " --> pdb=" O PRO C 342 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP C 346 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 348 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 353 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 4.227A pdb=" N CYS C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 393 through 396 No H-bonds generated for 'chain 'C' and resid 393 through 396' Processing helix chain 'C' and resid 400 through 410 removed outlier: 4.189A pdb=" N SER C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.637A pdb=" N THR C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 455 through 468 removed outlier: 3.518A pdb=" N ARG C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 549 through 555 Processing helix chain 'C' and resid 575 through 578 No H-bonds generated for 'chain 'C' and resid 575 through 578' Processing helix chain 'C' and resid 679 through 682 Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 726 through 734 removed outlier: 3.883A pdb=" N ASP C 733 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA C 734 " --> pdb=" O THR C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 783 No H-bonds generated for 'chain 'C' and resid 781 through 783' Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'F' and resid 27 through 46 removed outlier: 4.384A pdb=" N LEU F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS F 39 " --> pdb=" O GLN F 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 56 through 79 removed outlier: 4.125A pdb=" N GLU F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL F 77 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 135 Proline residue: F 131 - end of helix Processing helix chain 'F' and resid 164 through 179 removed outlier: 3.883A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER F 177 " --> pdb=" O TRP F 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP F 179 " --> pdb=" O PHE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 246 through 257 removed outlier: 3.855A pdb=" N LEU F 257 " --> pdb=" O ILE F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 320 through 331 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.584A pdb=" N GLU F 345 " --> pdb=" O PRO F 342 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP F 346 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY F 348 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 353 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 371 removed outlier: 4.227A pdb=" N CYS F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 393 through 396 No H-bonds generated for 'chain 'F' and resid 393 through 396' Processing helix chain 'F' and resid 400 through 410 removed outlier: 4.189A pdb=" N SER F 407 " --> pdb=" O SER F 403 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU F 410 " --> pdb=" O LEU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 422 removed outlier: 3.636A pdb=" N THR F 421 " --> pdb=" O SER F 417 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU F 422 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 443 Processing helix chain 'F' and resid 455 through 468 removed outlier: 3.518A pdb=" N ARG F 468 " --> pdb=" O GLY F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 Processing helix chain 'F' and resid 549 through 555 Processing helix chain 'F' and resid 575 through 578 No H-bonds generated for 'chain 'F' and resid 575 through 578' Processing helix chain 'F' and resid 679 through 682 Processing helix chain 'F' and resid 696 through 698 No H-bonds generated for 'chain 'F' and resid 696 through 698' Processing helix chain 'F' and resid 726 through 734 removed outlier: 3.883A pdb=" N ASP F 733 " --> pdb=" O ILE F 729 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA F 734 " --> pdb=" O THR F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 783 No H-bonds generated for 'chain 'F' and resid 781 through 783' Processing helix chain 'F' and resid 809 through 814 Processing helix chain 'G' and resid 27 through 46 removed outlier: 4.383A pdb=" N LEU G 34 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 56 through 79 removed outlier: 4.125A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 135 Proline residue: G 131 - end of helix Processing helix chain 'G' and resid 164 through 179 removed outlier: 3.883A pdb=" N ARG G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER G 177 " --> pdb=" O TRP G 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP G 179 " --> pdb=" O PHE G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 203 Processing helix chain 'G' and resid 206 through 211 Processing helix chain 'G' and resid 226 through 236 Processing helix chain 'G' and resid 246 through 257 removed outlier: 3.855A pdb=" N LEU G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'G' and resid 320 through 331 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.583A pdb=" N GLU G 345 " --> pdb=" O PRO G 342 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP G 346 " --> pdb=" O GLU G 343 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 347 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR G 353 " --> pdb=" O GLU G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 371 removed outlier: 4.228A pdb=" N CYS G 371 " --> pdb=" O GLY G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 384 Processing helix chain 'G' and resid 387 through 390 No H-bonds generated for 'chain 'G' and resid 387 through 390' Processing helix chain 'G' and resid 393 through 396 No H-bonds generated for 'chain 'G' and resid 393 through 396' Processing helix chain 'G' and resid 400 through 410 removed outlier: 4.189A pdb=" N SER G 407 " --> pdb=" O SER G 403 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 422 removed outlier: 3.637A pdb=" N THR G 421 " --> pdb=" O SER G 417 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU G 422 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 443 Processing helix chain 'G' and resid 455 through 468 removed outlier: 3.518A pdb=" N ARG G 468 " --> pdb=" O GLY G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 499 Processing helix chain 'G' and resid 549 through 555 Processing helix chain 'G' and resid 575 through 578 No H-bonds generated for 'chain 'G' and resid 575 through 578' Processing helix chain 'G' and resid 679 through 682 Processing helix chain 'G' and resid 696 through 698 No H-bonds generated for 'chain 'G' and resid 696 through 698' Processing helix chain 'G' and resid 726 through 734 removed outlier: 3.883A pdb=" N ASP G 733 " --> pdb=" O ILE G 729 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA G 734 " --> pdb=" O THR G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 781 through 783 No H-bonds generated for 'chain 'G' and resid 781 through 783' Processing helix chain 'G' and resid 809 through 814 Processing helix chain 'L' and resid 27 through 46 removed outlier: 4.383A pdb=" N LEU L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS L 39 " --> pdb=" O GLN L 35 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 50 No H-bonds generated for 'chain 'L' and resid 48 through 50' Processing helix chain 'L' and resid 56 through 79 removed outlier: 4.126A pdb=" N GLU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL L 77 " --> pdb=" O GLU L 73 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS L 79 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 135 Proline residue: L 131 - end of helix Processing helix chain 'L' and resid 164 through 179 removed outlier: 3.883A pdb=" N ARG L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER L 177 " --> pdb=" O TRP L 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN L 178 " --> pdb=" O LEU L 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP L 179 " --> pdb=" O PHE L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 206 through 211 Processing helix chain 'L' and resid 226 through 236 Processing helix chain 'L' and resid 246 through 257 removed outlier: 3.855A pdb=" N LEU L 257 " --> pdb=" O ILE L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 280 Processing helix chain 'L' and resid 300 through 304 Processing helix chain 'L' and resid 320 through 331 Processing helix chain 'L' and resid 342 through 355 removed outlier: 3.583A pdb=" N GLU L 345 " --> pdb=" O PRO L 342 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP L 346 " --> pdb=" O GLU L 343 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL L 347 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 348 " --> pdb=" O GLU L 345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR L 353 " --> pdb=" O GLU L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 371 removed outlier: 4.228A pdb=" N CYS L 371 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 384 Processing helix chain 'L' and resid 387 through 390 No H-bonds generated for 'chain 'L' and resid 387 through 390' Processing helix chain 'L' and resid 393 through 396 No H-bonds generated for 'chain 'L' and resid 393 through 396' Processing helix chain 'L' and resid 400 through 410 removed outlier: 4.189A pdb=" N SER L 407 " --> pdb=" O SER L 403 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU L 410 " --> pdb=" O LEU L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 422 removed outlier: 3.637A pdb=" N THR L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU L 422 " --> pdb=" O CYS L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 443 Processing helix chain 'L' and resid 455 through 468 removed outlier: 3.518A pdb=" N ARG L 468 " --> pdb=" O GLY L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 499 Processing helix chain 'L' and resid 549 through 555 Processing helix chain 'L' and resid 575 through 578 No H-bonds generated for 'chain 'L' and resid 575 through 578' Processing helix chain 'L' and resid 679 through 682 Processing helix chain 'L' and resid 696 through 698 No H-bonds generated for 'chain 'L' and resid 696 through 698' Processing helix chain 'L' and resid 726 through 734 removed outlier: 3.883A pdb=" N ASP L 733 " --> pdb=" O ILE L 729 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA L 734 " --> pdb=" O THR L 730 " (cutoff:3.500A) Processing helix chain 'L' and resid 781 through 783 No H-bonds generated for 'chain 'L' and resid 781 through 783' Processing helix chain 'L' and resid 809 through 814 Processing helix chain 'O' and resid 27 through 46 removed outlier: 4.383A pdb=" N LEU O 34 " --> pdb=" O GLN O 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS O 39 " --> pdb=" O GLN O 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER O 43 " --> pdb=" O LYS O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 50 No H-bonds generated for 'chain 'O' and resid 48 through 50' Processing helix chain 'O' and resid 56 through 79 removed outlier: 4.125A pdb=" N GLU O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS O 79 " --> pdb=" O ILE O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 135 Proline residue: O 131 - end of helix Processing helix chain 'O' and resid 164 through 179 removed outlier: 3.882A pdb=" N ARG O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER O 177 " --> pdb=" O TRP O 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN O 178 " --> pdb=" O LEU O 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP O 179 " --> pdb=" O PHE O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 203 Processing helix chain 'O' and resid 206 through 211 Processing helix chain 'O' and resid 226 through 236 Processing helix chain 'O' and resid 246 through 257 removed outlier: 3.854A pdb=" N LEU O 257 " --> pdb=" O ILE O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 274 through 280 Processing helix chain 'O' and resid 300 through 304 Processing helix chain 'O' and resid 320 through 331 Processing helix chain 'O' and resid 342 through 355 removed outlier: 3.583A pdb=" N GLU O 345 " --> pdb=" O PRO O 342 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP O 346 " --> pdb=" O GLU O 343 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL O 347 " --> pdb=" O LEU O 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY O 348 " --> pdb=" O GLU O 345 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR O 353 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 371 removed outlier: 4.228A pdb=" N CYS O 371 " --> pdb=" O GLY O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 384 Processing helix chain 'O' and resid 387 through 390 No H-bonds generated for 'chain 'O' and resid 387 through 390' Processing helix chain 'O' and resid 393 through 396 No H-bonds generated for 'chain 'O' and resid 393 through 396' Processing helix chain 'O' and resid 400 through 410 removed outlier: 4.189A pdb=" N SER O 407 " --> pdb=" O SER O 403 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU O 410 " --> pdb=" O LEU O 406 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 422 removed outlier: 3.636A pdb=" N THR O 421 " --> pdb=" O SER O 417 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU O 422 " --> pdb=" O CYS O 418 " (cutoff:3.500A) Processing helix chain 'O' and resid 433 through 443 Processing helix chain 'O' and resid 455 through 468 removed outlier: 3.517A pdb=" N ARG O 468 " --> pdb=" O GLY O 464 " (cutoff:3.500A) Processing helix chain 'O' and resid 489 through 499 Processing helix chain 'O' and resid 549 through 555 Processing helix chain 'O' and resid 575 through 578 No H-bonds generated for 'chain 'O' and resid 575 through 578' Processing helix chain 'O' and resid 679 through 682 Processing helix chain 'O' and resid 696 through 698 No H-bonds generated for 'chain 'O' and resid 696 through 698' Processing helix chain 'O' and resid 726 through 734 removed outlier: 3.882A pdb=" N ASP O 733 " --> pdb=" O ILE O 729 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA O 734 " --> pdb=" O THR O 730 " (cutoff:3.500A) Processing helix chain 'O' and resid 781 through 783 No H-bonds generated for 'chain 'O' and resid 781 through 783' Processing helix chain 'O' and resid 809 through 814 Processing sheet with id= A, first strand: chain 'B' and resid 123 through 127 removed outlier: 6.892A pdb=" N VAL B 136 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS B 126 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 134 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG B 76 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 65 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 183 through 188 removed outlier: 6.337A pdb=" N ARG C 214 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 265 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 216 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP C 267 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 218 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL C 269 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 514 through 517 removed outlier: 6.211A pdb=" N GLY C 534 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 517 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 536 " --> pdb=" O ILE C 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 563 through 565 removed outlier: 6.038A pdb=" N CYS C 590 " --> pdb=" O LEU C 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 614 through 616 removed outlier: 6.084A pdb=" N VAL C 638 " --> pdb=" O LEU C 615 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 662 " --> pdb=" O LEU C 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 688 through 692 removed outlier: 6.382A pdb=" N SER C 715 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 691 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER C 717 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU C 743 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE C 718 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 745 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 768 " --> pdb=" O LEU C 744 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N LEU C 746 " --> pdb=" O TYR C 768 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER C 770 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY C 795 " --> pdb=" O MET C 769 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE C 771 " --> pdb=" O GLY C 795 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET C 797 " --> pdb=" O ILE C 771 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR C 820 " --> pdb=" O LEU C 796 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU C 798 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 822 " --> pdb=" O LEU C 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 472 through 475 removed outlier: 7.166A pdb=" N THR C 484 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 183 through 188 removed outlier: 6.338A pdb=" N ARG F 214 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL F 265 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE F 216 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP F 267 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 218 " --> pdb=" O ASP F 267 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL F 269 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 514 through 517 removed outlier: 6.211A pdb=" N GLY F 534 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE F 517 " --> pdb=" O GLY F 534 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 536 " --> pdb=" O ILE F 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 563 through 565 removed outlier: 6.039A pdb=" N CYS F 590 " --> pdb=" O LEU F 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 614 through 616 removed outlier: 6.084A pdb=" N VAL F 638 " --> pdb=" O LEU F 615 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL F 662 " --> pdb=" O LEU F 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 688 through 692 removed outlier: 6.382A pdb=" N SER F 715 " --> pdb=" O LEU F 689 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU F 691 " --> pdb=" O SER F 715 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER F 717 " --> pdb=" O LEU F 691 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU F 743 " --> pdb=" O ILE F 716 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE F 718 " --> pdb=" O GLU F 743 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER F 745 " --> pdb=" O ILE F 718 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR F 768 " --> pdb=" O LEU F 744 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N LEU F 746 " --> pdb=" O TYR F 768 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER F 770 " --> pdb=" O LEU F 746 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY F 795 " --> pdb=" O MET F 769 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE F 771 " --> pdb=" O GLY F 795 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET F 797 " --> pdb=" O ILE F 771 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR F 820 " --> pdb=" O LEU F 796 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU F 798 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR F 822 " --> pdb=" O LEU F 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 472 through 475 removed outlier: 7.166A pdb=" N THR F 484 " --> pdb=" O VAL F 474 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 183 through 188 removed outlier: 6.337A pdb=" N ARG G 214 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL G 265 " --> pdb=" O ARG G 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE G 216 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP G 267 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL G 218 " --> pdb=" O ASP G 267 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL G 269 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 514 through 517 removed outlier: 6.211A pdb=" N GLY G 534 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE G 517 " --> pdb=" O GLY G 534 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL G 536 " --> pdb=" O ILE G 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 563 through 565 removed outlier: 6.038A pdb=" N CYS G 590 " --> pdb=" O LEU G 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 614 through 616 removed outlier: 6.085A pdb=" N VAL G 638 " --> pdb=" O LEU G 615 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL G 662 " --> pdb=" O LEU G 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'G' and resid 688 through 692 removed outlier: 6.383A pdb=" N SER G 715 " --> pdb=" O LEU G 689 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU G 691 " --> pdb=" O SER G 715 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER G 717 " --> pdb=" O LEU G 691 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU G 743 " --> pdb=" O ILE G 716 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE G 718 " --> pdb=" O GLU G 743 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER G 745 " --> pdb=" O ILE G 718 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR G 768 " --> pdb=" O LEU G 744 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU G 746 " --> pdb=" O TYR G 768 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER G 770 " --> pdb=" O LEU G 746 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY G 795 " --> pdb=" O MET G 769 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE G 771 " --> pdb=" O GLY G 795 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET G 797 " --> pdb=" O ILE G 771 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR G 820 " --> pdb=" O LEU G 796 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU G 798 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR G 822 " --> pdb=" O LEU G 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'G' and resid 472 through 475 removed outlier: 7.165A pdb=" N THR G 484 " --> pdb=" O VAL G 474 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 183 through 188 removed outlier: 6.338A pdb=" N ARG L 214 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL L 265 " --> pdb=" O ARG L 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE L 216 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP L 267 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL L 218 " --> pdb=" O ASP L 267 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL L 269 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 514 through 517 removed outlier: 6.210A pdb=" N GLY L 534 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE L 517 " --> pdb=" O GLY L 534 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL L 536 " --> pdb=" O ILE L 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'L' and resid 563 through 565 removed outlier: 6.038A pdb=" N CYS L 590 " --> pdb=" O LEU L 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'L' and resid 614 through 616 removed outlier: 6.084A pdb=" N VAL L 638 " --> pdb=" O LEU L 615 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL L 662 " --> pdb=" O LEU L 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 688 through 692 removed outlier: 6.383A pdb=" N SER L 715 " --> pdb=" O LEU L 689 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU L 691 " --> pdb=" O SER L 715 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER L 717 " --> pdb=" O LEU L 691 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU L 743 " --> pdb=" O ILE L 716 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE L 718 " --> pdb=" O GLU L 743 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER L 745 " --> pdb=" O ILE L 718 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR L 768 " --> pdb=" O LEU L 744 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU L 746 " --> pdb=" O TYR L 768 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER L 770 " --> pdb=" O LEU L 746 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY L 795 " --> pdb=" O MET L 769 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE L 771 " --> pdb=" O GLY L 795 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET L 797 " --> pdb=" O ILE L 771 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR L 820 " --> pdb=" O LEU L 796 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU L 798 " --> pdb=" O THR L 820 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR L 822 " --> pdb=" O LEU L 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'L' and resid 472 through 475 removed outlier: 7.166A pdb=" N THR L 484 " --> pdb=" O VAL L 474 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 183 through 188 removed outlier: 6.338A pdb=" N ARG O 214 " --> pdb=" O LEU O 263 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL O 265 " --> pdb=" O ARG O 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE O 216 " --> pdb=" O VAL O 265 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP O 267 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL O 218 " --> pdb=" O ASP O 267 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL O 269 " --> pdb=" O VAL O 218 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 514 through 517 removed outlier: 6.210A pdb=" N GLY O 534 " --> pdb=" O LEU O 515 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE O 517 " --> pdb=" O GLY O 534 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL O 536 " --> pdb=" O ILE O 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'O' and resid 563 through 565 removed outlier: 6.039A pdb=" N CYS O 590 " --> pdb=" O LEU O 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'O' and resid 614 through 616 removed outlier: 6.084A pdb=" N VAL O 638 " --> pdb=" O LEU O 615 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL O 662 " --> pdb=" O LEU O 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'O' and resid 688 through 692 removed outlier: 6.382A pdb=" N SER O 715 " --> pdb=" O LEU O 689 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU O 691 " --> pdb=" O SER O 715 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER O 717 " --> pdb=" O LEU O 691 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU O 743 " --> pdb=" O ILE O 716 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE O 718 " --> pdb=" O GLU O 743 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER O 745 " --> pdb=" O ILE O 718 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR O 768 " --> pdb=" O LEU O 744 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N LEU O 746 " --> pdb=" O TYR O 768 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER O 770 " --> pdb=" O LEU O 746 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY O 795 " --> pdb=" O MET O 769 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE O 771 " --> pdb=" O GLY O 795 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET O 797 " --> pdb=" O ILE O 771 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR O 820 " --> pdb=" O LEU O 796 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU O 798 " --> pdb=" O THR O 820 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR O 822 " --> pdb=" O LEU O 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'O' and resid 472 through 475 removed outlier: 7.166A pdb=" N THR O 484 " --> pdb=" O VAL O 474 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 14.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6066 1.31 - 1.44: 9310 1.44 - 1.57: 20957 1.57 - 1.70: 31 1.70 - 1.82: 319 Bond restraints: 36683 Sorted by residual: bond pdb=" C2' BQO A 502 " pdb=" C3' BQO A 502 " ideal model delta sigma weight residual 1.635 1.463 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C1' BQO A 502 " pdb=" C2' BQO A 502 " ideal model delta sigma weight residual 1.314 1.480 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" C2 BQO A 502 " pdb=" N1 BQO A 502 " ideal model delta sigma weight residual 1.512 1.346 0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" C3 BQO A 502 " pdb=" C3' BQO A 502 " ideal model delta sigma weight residual 1.322 1.486 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C5 BQO A 502 " pdb=" C6 BQO A 502 " ideal model delta sigma weight residual 1.502 1.352 0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 36678 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.88: 582 104.88 - 112.19: 17643 112.19 - 119.50: 13792 119.50 - 126.81: 16965 126.81 - 134.13: 600 Bond angle restraints: 49582 Sorted by residual: angle pdb=" PB DTP G 901 " pdb=" O3B DTP G 901 " pdb=" PG DTP G 901 " ideal model delta sigma weight residual 139.87 125.31 14.56 1.00e+00 1.00e+00 2.12e+02 angle pdb=" PA DTP F 901 " pdb=" O3A DTP F 901 " pdb=" PB DTP F 901 " ideal model delta sigma weight residual 136.83 122.70 14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" PB DTP F 901 " pdb=" O3B DTP F 901 " pdb=" PG DTP F 901 " ideal model delta sigma weight residual 139.87 125.90 13.97 1.00e+00 1.00e+00 1.95e+02 angle pdb=" PA DTP C 901 " pdb=" O3A DTP C 901 " pdb=" PB DTP C 901 " ideal model delta sigma weight residual 136.83 123.58 13.25 1.00e+00 1.00e+00 1.76e+02 angle pdb=" PA DTP O 901 " pdb=" O3A DTP O 901 " pdb=" PB DTP O 901 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 ... (remaining 49577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 21357 22.41 - 44.81: 907 44.81 - 67.22: 78 67.22 - 89.63: 32 89.63 - 112.04: 4 Dihedral angle restraints: 22378 sinusoidal: 9400 harmonic: 12978 Sorted by residual: dihedral pdb=" CA PRO B 131 " pdb=" C PRO B 131 " pdb=" N PHE B 132 " pdb=" CA PHE B 132 " ideal model delta harmonic sigma weight residual -180.00 -104.42 -75.58 0 5.00e+00 4.00e-02 2.29e+02 dihedral pdb=" CA ASN G 506 " pdb=" C ASN G 506 " pdb=" N PRO G 507 " pdb=" CA PRO G 507 " ideal model delta harmonic sigma weight residual 180.00 -114.40 -65.60 0 5.00e+00 4.00e-02 1.72e+02 dihedral pdb=" CA ASN F 506 " pdb=" C ASN F 506 " pdb=" N PRO F 507 " pdb=" CA PRO F 507 " ideal model delta harmonic sigma weight residual -180.00 -114.41 -65.59 0 5.00e+00 4.00e-02 1.72e+02 ... (remaining 22375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4317 0.069 - 0.139: 1021 0.139 - 0.208: 189 0.208 - 0.277: 28 0.277 - 0.347: 8 Chirality restraints: 5563 Sorted by residual: chirality pdb=" CA THR B 231 " pdb=" N THR B 231 " pdb=" C THR B 231 " pdb=" CB THR B 231 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE C 630 " pdb=" CA ILE C 630 " pdb=" CG1 ILE C 630 " pdb=" CG2 ILE C 630 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB ILE B 296 " pdb=" CA ILE B 296 " pdb=" CG1 ILE B 296 " pdb=" CG2 ILE B 296 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5560 not shown) Planarity restraints: 6285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 132 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO B 133 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 80 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU B 80 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU B 80 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP B 81 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O 506 " -0.045 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO O 507 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO O 507 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 507 " -0.038 5.00e-02 4.00e+02 ... (remaining 6282 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1091 2.69 - 3.24: 35180 3.24 - 3.79: 57515 3.79 - 4.35: 74636 4.35 - 4.90: 120900 Nonbonded interactions: 289322 Sorted by model distance: nonbonded pdb=" OE2 GLU F 472 " pdb=" NZ LYS F 486 " model vdw 2.132 2.520 nonbonded pdb=" OE2 GLU C 472 " pdb=" NZ LYS C 486 " model vdw 2.132 2.520 nonbonded pdb=" OE2 GLU G 472 " pdb=" NZ LYS G 486 " model vdw 2.132 2.520 nonbonded pdb=" OE2 GLU L 472 " pdb=" NZ LYS L 486 " model vdw 2.132 2.520 nonbonded pdb=" OE2 GLU O 472 " pdb=" NZ LYS O 486 " model vdw 2.133 2.520 ... (remaining 289317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.040 Extract box with map and model: 11.270 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 91.370 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.007 0.172 36683 Z= 0.476 Angle : 1.132 14.562 49582 Z= 0.622 Chirality : 0.063 0.347 5563 Planarity : 0.008 0.125 6283 Dihedral : 12.303 112.035 13964 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.09 % Favored : 89.63 % Rotamer: Outliers : 0.72 % Allowed : 6.30 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.42 % 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: -4.37 (0.10), residues: 4428 helix: -2.55 (0.09), residues: 1642 sheet: -1.89 (0.21), residues: 508 loop : -3.50 (0.10), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 162 HIS 0.017 0.003 HIS O 438 PHE 0.030 0.003 PHE O 203 TYR 0.025 0.003 TYR F 256 ARG 0.006 0.001 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 955 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.8748 (mp0) cc_final: 0.8332 (mp0) REVERT: A 196 LYS cc_start: 0.8320 (mttt) cc_final: 0.7821 (mttp) REVERT: A 203 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7741 (tmmt) REVERT: A 216 ILE cc_start: 0.8158 (mt) cc_final: 0.7867 (pt) REVERT: A 219 ASP cc_start: 0.7242 (t70) cc_final: 0.6900 (p0) REVERT: B 107 ASP cc_start: 0.8451 (t0) cc_final: 0.7993 (t0) REVERT: C 116 GLN cc_start: 0.9144 (tt0) cc_final: 0.8874 (tt0) REVERT: C 133 PHE cc_start: 0.8997 (m-80) cc_final: 0.8722 (m-80) REVERT: C 225 THR cc_start: 0.8807 (t) cc_final: 0.8025 (p) REVERT: C 335 ASN cc_start: 0.7623 (t0) cc_final: 0.7393 (t0) REVERT: C 405 GLN cc_start: 0.8379 (tt0) cc_final: 0.8115 (tt0) REVERT: C 409 ASP cc_start: 0.8332 (m-30) cc_final: 0.8054 (m-30) REVERT: C 561 LEU cc_start: 0.9264 (tm) cc_final: 0.9037 (tp) REVERT: C 602 PHE cc_start: 0.7583 (p90) cc_final: 0.7183 (p90) REVERT: C 612 LEU cc_start: 0.8704 (tt) cc_final: 0.8492 (tp) REVERT: C 722 ASP cc_start: 0.7201 (t0) cc_final: 0.6961 (t0) REVERT: F 125 ILE cc_start: 0.9199 (pp) cc_final: 0.8808 (mt) REVERT: F 237 LEU cc_start: 0.9004 (mt) cc_final: 0.8707 (mt) REVERT: F 515 LEU cc_start: 0.9152 (tm) cc_final: 0.8638 (tt) REVERT: F 763 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9058 (pp) REVERT: G 67 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7885 (tp30) REVERT: G 117 GLU cc_start: 0.8411 (pt0) cc_final: 0.8003 (pp20) REVERT: G 125 ILE cc_start: 0.9238 (pp) cc_final: 0.8989 (mt) REVERT: G 130 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7185 (tm-30) REVERT: G 225 THR cc_start: 0.8583 (t) cc_final: 0.7869 (p) REVERT: G 336 ASP cc_start: 0.7579 (t0) cc_final: 0.7352 (t0) REVERT: G 405 GLN cc_start: 0.8237 (tt0) cc_final: 0.7644 (tp40) REVERT: G 434 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8276 (tp-100) REVERT: G 443 GLU cc_start: 0.8849 (pp20) cc_final: 0.8398 (pp20) REVERT: G 497 ASP cc_start: 0.8136 (t70) cc_final: 0.7641 (t70) REVERT: G 511 ASN cc_start: 0.8377 (t160) cc_final: 0.8069 (t0) REVERT: G 546 LYS cc_start: 0.7936 (tptp) cc_final: 0.7725 (mmtt) REVERT: G 703 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6674 (mt-10) REVERT: G 763 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8426 (pp) REVERT: G 779 MET cc_start: 0.7776 (mmt) cc_final: 0.7136 (pmm) REVERT: L 61 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8364 (pt) REVERT: L 67 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7734 (tp30) REVERT: L 184 ILE cc_start: 0.8605 (pt) cc_final: 0.8199 (mt) REVERT: L 225 THR cc_start: 0.8416 (t) cc_final: 0.7907 (p) REVERT: L 410 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7278 (mt-10) REVERT: L 490 MET cc_start: 0.8333 (mmm) cc_final: 0.8085 (mmp) REVERT: L 497 ASP cc_start: 0.8316 (t70) cc_final: 0.7864 (t0) REVERT: L 511 ASN cc_start: 0.8290 (t160) cc_final: 0.7833 (t0) REVERT: L 624 LYS cc_start: 0.8757 (mttp) cc_final: 0.8498 (mttt) REVERT: L 640 ASP cc_start: 0.8189 (t0) cc_final: 0.7851 (t0) REVERT: O 32 GLU cc_start: 0.8618 (pp20) cc_final: 0.8388 (pt0) REVERT: O 71 GLU cc_start: 0.8667 (tp30) cc_final: 0.8364 (tp30) REVERT: O 113 LYS cc_start: 0.9039 (mttt) cc_final: 0.8561 (mmtm) REVERT: O 116 GLN cc_start: 0.8985 (tt0) cc_final: 0.8562 (tt0) REVERT: O 120 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8166 (mt-10) REVERT: O 125 ILE cc_start: 0.9290 (pp) cc_final: 0.8978 (mt) REVERT: O 226 GLU cc_start: 0.8577 (mp0) cc_final: 0.8308 (mp0) REVERT: O 279 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8676 (mtpt) REVERT: O 417 SER cc_start: 0.9079 (m) cc_final: 0.8741 (p) REVERT: O 567 SER cc_start: 0.8453 (m) cc_final: 0.8237 (p) REVERT: O 570 ILE cc_start: 0.9049 (mt) cc_final: 0.8826 (mm) REVERT: O 634 LYS cc_start: 0.8669 (pmtt) cc_final: 0.8466 (ptpp) outliers start: 29 outliers final: 6 residues processed: 975 average time/residue: 0.5567 time to fit residues: 845.5544 Evaluate side-chains 485 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 476 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 741 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 376 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 115 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 349 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 260 optimal weight: 0.8980 chunk 405 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN B 119 ASN B 311 GLN C 288 GLN ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN C 672 ASN C 673 ASN C 698 GLN C 742 HIS C 747 GLN F 236 ASN F 273 ASN F 288 GLN F 322 ASN F 335 ASN F 377 HIS F 627 GLN F 672 ASN F 673 ASN ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 742 HIS F 747 GLN F 786 ASN G 128 GLN G 222 GLN G 288 GLN G 322 ASN G 511 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 ASN G 673 ASN ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 742 HIS G 747 GLN L 288 GLN L 322 ASN L 335 ASN L 399 ASN L 435 GLN L 511 ASN L 627 GLN L 672 ASN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 742 HIS L 747 GLN L 812 GLN O 30 GLN O 128 GLN ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 288 GLN O 322 ASN O 435 GLN O 625 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 672 ASN O 673 ASN ** O 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 742 HIS O 747 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36683 Z= 0.238 Angle : 0.696 11.543 49582 Z= 0.363 Chirality : 0.046 0.204 5563 Planarity : 0.005 0.104 6283 Dihedral : 9.829 98.676 5012 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.26 % Favored : 90.56 % Rotamer: Outliers : 2.40 % Allowed : 12.33 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.30 % 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: -3.12 (0.11), residues: 4428 helix: -1.06 (0.12), residues: 1680 sheet: -1.72 (0.21), residues: 505 loop : -3.05 (0.11), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 22 HIS 0.010 0.001 HIS C 597 PHE 0.020 0.002 PHE F 748 TYR 0.023 0.002 TYR A 143 ARG 0.007 0.001 ARG F 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 565 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ILE cc_start: 0.8221 (mt) cc_final: 0.7841 (mm) REVERT: B 107 ASP cc_start: 0.8521 (t0) cc_final: 0.8295 (t0) REVERT: B 171 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 195 MET cc_start: 0.8750 (mmt) cc_final: 0.8420 (mpp) REVERT: C 130 GLU cc_start: 0.8415 (tt0) cc_final: 0.8178 (tt0) REVERT: C 133 PHE cc_start: 0.8953 (m-80) cc_final: 0.8659 (m-80) REVERT: C 184 ILE cc_start: 0.8556 (pt) cc_final: 0.8339 (mt) REVERT: C 602 PHE cc_start: 0.7751 (p90) cc_final: 0.7512 (p90) REVERT: C 650 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: C 722 ASP cc_start: 0.7284 (t0) cc_final: 0.7009 (t0) REVERT: F 130 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7886 (tm-30) REVERT: F 237 LEU cc_start: 0.9128 (mt) cc_final: 0.8864 (mt) REVERT: F 459 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7624 (mm-30) REVERT: F 515 LEU cc_start: 0.9044 (tm) cc_final: 0.8652 (tt) REVERT: F 604 ARG cc_start: 0.7852 (tmm-80) cc_final: 0.7647 (ttp80) REVERT: F 648 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: F 687 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7286 (mtp85) REVERT: F 763 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8996 (pp) REVERT: G 32 GLU cc_start: 0.8452 (pp20) cc_final: 0.8211 (pp20) REVERT: G 67 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7847 (tp30) REVERT: G 130 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7493 (tm-30) REVERT: G 266 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8354 (mtp) REVERT: G 405 GLN cc_start: 0.8079 (tt0) cc_final: 0.7661 (tp40) REVERT: G 434 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8220 (tp-100) REVERT: G 443 GLU cc_start: 0.8804 (pp20) cc_final: 0.8197 (pp20) REVERT: G 497 ASP cc_start: 0.8207 (t70) cc_final: 0.7750 (t70) REVERT: G 511 ASN cc_start: 0.8322 (t0) cc_final: 0.7921 (t0) REVERT: G 546 LYS cc_start: 0.8045 (tptp) cc_final: 0.7735 (mmtt) REVERT: G 779 MET cc_start: 0.7605 (mmt) cc_final: 0.7345 (pmm) REVERT: G 805 ASP cc_start: 0.7273 (m-30) cc_final: 0.6771 (t70) REVERT: L 33 ASP cc_start: 0.8271 (p0) cc_final: 0.8041 (p0) REVERT: L 272 LYS cc_start: 0.8544 (tppt) cc_final: 0.8183 (tppt) REVERT: L 497 ASP cc_start: 0.8322 (t70) cc_final: 0.8027 (t0) REVERT: L 640 ASP cc_start: 0.8250 (t0) cc_final: 0.7678 (t0) REVERT: L 666 PHE cc_start: 0.7937 (t80) cc_final: 0.7529 (t80) REVERT: O 71 GLU cc_start: 0.8643 (tp30) cc_final: 0.8345 (tp30) REVERT: O 113 LYS cc_start: 0.8963 (mttt) cc_final: 0.8638 (mmtm) REVERT: O 116 GLN cc_start: 0.9022 (tt0) cc_final: 0.8681 (tt0) REVERT: O 120 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8259 (mt-10) REVERT: O 279 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8693 (mtpp) REVERT: O 417 SER cc_start: 0.9106 (m) cc_final: 0.8743 (p) REVERT: O 567 SER cc_start: 0.8377 (m) cc_final: 0.8067 (p) REVERT: O 634 LYS cc_start: 0.8735 (pmtt) cc_final: 0.8478 (ptpp) outliers start: 97 outliers final: 47 residues processed: 627 average time/residue: 0.4666 time to fit residues: 478.3955 Evaluate side-chains 502 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 450 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 489 ASP Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 683 LEU Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 803 ASP Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain O residue 30 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 278 ASP Chi-restraints excluded: chain O residue 435 GLN Chi-restraints excluded: chain O residue 590 CYS Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 726 ASP Chi-restraints excluded: chain O residue 741 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 225 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 337 optimal weight: 0.5980 chunk 275 optimal weight: 0.0370 chunk 111 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 438 optimal weight: 7.9990 chunk 361 optimal weight: 3.9990 chunk 402 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 251 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN F 627 GLN ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN O 335 ASN O 435 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 698 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36683 Z= 0.207 Angle : 0.643 9.624 49582 Z= 0.333 Chirality : 0.045 0.171 5563 Planarity : 0.005 0.104 6283 Dihedral : 9.039 98.412 5004 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.55 % Favored : 90.29 % Rotamer: Outliers : 3.46 % Allowed : 13.20 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.28 % 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: -2.58 (0.12), residues: 4428 helix: -0.49 (0.12), residues: 1741 sheet: -1.54 (0.22), residues: 495 loop : -2.87 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 448 HIS 0.007 0.001 HIS C 597 PHE 0.017 0.001 PHE F 748 TYR 0.018 0.001 TYR A 143 ARG 0.005 0.000 ARG L 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 515 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8738 (m-30) cc_final: 0.8207 (m-30) REVERT: B 195 MET cc_start: 0.8743 (mmt) cc_final: 0.8401 (mpp) REVERT: B 296 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6712 (mp) REVERT: B 297 ASP cc_start: 0.6872 (m-30) cc_final: 0.6635 (m-30) REVERT: C 109 TYR cc_start: 0.8588 (t80) cc_final: 0.8104 (t80) REVERT: C 113 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9069 (mmmt) REVERT: C 130 GLU cc_start: 0.8443 (tt0) cc_final: 0.8182 (tt0) REVERT: C 203 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7569 (p90) REVERT: C 428 ASP cc_start: 0.8109 (m-30) cc_final: 0.7863 (m-30) REVERT: C 602 PHE cc_start: 0.7801 (p90) cc_final: 0.7515 (p90) REVERT: C 650 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: C 722 ASP cc_start: 0.7405 (t0) cc_final: 0.7068 (t0) REVERT: C 733 ASP cc_start: 0.8089 (m-30) cc_final: 0.7837 (t0) REVERT: F 130 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 237 LEU cc_start: 0.9134 (mt) cc_final: 0.8889 (mt) REVERT: F 515 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8841 (tt) REVERT: F 604 ARG cc_start: 0.7997 (tmm-80) cc_final: 0.7772 (ttp80) REVERT: F 648 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: F 687 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7418 (mtp85) REVERT: F 722 ASP cc_start: 0.8111 (m-30) cc_final: 0.7564 (p0) REVERT: F 733 ASP cc_start: 0.8117 (m-30) cc_final: 0.7886 (t0) REVERT: F 743 GLU cc_start: 0.7632 (tt0) cc_final: 0.7349 (pt0) REVERT: F 763 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9089 (pp) REVERT: F 830 GLU cc_start: 0.7762 (mp0) cc_final: 0.7395 (mp0) REVERT: G 32 GLU cc_start: 0.8390 (pp20) cc_final: 0.8137 (pp20) REVERT: G 67 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7799 (tp30) REVERT: G 130 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7495 (tm-30) REVERT: G 266 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: G 405 GLN cc_start: 0.8008 (tt0) cc_final: 0.7679 (tp40) REVERT: G 434 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8139 (tp-100) REVERT: G 443 GLU cc_start: 0.8699 (pp20) cc_final: 0.8172 (pp20) REVERT: G 511 ASN cc_start: 0.8384 (t0) cc_final: 0.7936 (t0) REVERT: G 546 LYS cc_start: 0.7994 (tptp) cc_final: 0.7695 (mmtt) REVERT: G 565 ASP cc_start: 0.8116 (p0) cc_final: 0.7872 (p0) REVERT: G 779 MET cc_start: 0.7594 (mmt) cc_final: 0.7342 (pmm) REVERT: L 33 ASP cc_start: 0.8266 (p0) cc_final: 0.8039 (p0) REVERT: L 53 ARG cc_start: 0.6927 (ttt90) cc_final: 0.6699 (tpt90) REVERT: L 203 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7748 (p90) REVERT: L 401 MET cc_start: 0.8250 (mmp) cc_final: 0.7661 (mmt) REVERT: L 497 ASP cc_start: 0.8413 (t70) cc_final: 0.8113 (t0) REVERT: L 506 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7123 (t0) REVERT: L 666 PHE cc_start: 0.7992 (t80) cc_final: 0.7519 (t80) REVERT: L 797 MET cc_start: 0.8471 (ttm) cc_final: 0.8160 (tpp) REVERT: O 71 GLU cc_start: 0.8651 (tp30) cc_final: 0.8329 (tp30) REVERT: O 113 LYS cc_start: 0.9004 (mttt) cc_final: 0.8629 (mmtm) REVERT: O 116 GLN cc_start: 0.8993 (tt0) cc_final: 0.8546 (tt0) REVERT: O 120 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8187 (mt-10) REVERT: O 184 ILE cc_start: 0.8386 (pt) cc_final: 0.8179 (mt) REVERT: O 279 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8673 (mttt) REVERT: O 417 SER cc_start: 0.9100 (m) cc_final: 0.8758 (p) REVERT: O 521 PHE cc_start: 0.6621 (m-80) cc_final: 0.6023 (m-80) REVERT: O 634 LYS cc_start: 0.8739 (pmtt) cc_final: 0.8471 (ptpp) outliers start: 140 outliers final: 71 residues processed: 608 average time/residue: 0.4604 time to fit residues: 462.2531 Evaluate side-chains 529 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 447 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 73 GLU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 335 ASN Chi-restraints excluded: chain L residue 506 ASN Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 726 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 400 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 407 optimal weight: 0.9980 chunk 431 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 385 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 GLN O 128 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36683 Z= 0.196 Angle : 0.629 11.618 49582 Z= 0.321 Chirality : 0.045 0.176 5563 Planarity : 0.005 0.100 6283 Dihedral : 8.238 104.306 5000 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.58 % Favored : 90.27 % Rotamer: Outliers : 3.76 % Allowed : 14.41 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.23 % 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: -2.25 (0.12), residues: 4428 helix: -0.23 (0.13), residues: 1779 sheet: -1.38 (0.23), residues: 515 loop : -2.70 (0.12), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 757 HIS 0.006 0.001 HIS C 597 PHE 0.030 0.001 PHE O 504 TYR 0.024 0.001 TYR A 143 ARG 0.004 0.000 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 508 time to evaluate : 4.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.6474 (t-100) cc_final: 0.6157 (t-100) REVERT: A 220 PHE cc_start: 0.8004 (t80) cc_final: 0.7609 (t80) REVERT: A 226 LEU cc_start: 0.8170 (mt) cc_final: 0.7798 (mp) REVERT: A 278 ASP cc_start: 0.8723 (m-30) cc_final: 0.8321 (m-30) REVERT: A 359 MET cc_start: 0.7741 (mpp) cc_final: 0.6701 (ptt) REVERT: B 130 PHE cc_start: 0.7551 (m-10) cc_final: 0.7325 (m-10) REVERT: B 171 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7400 (mt-10) REVERT: B 195 MET cc_start: 0.8654 (mmt) cc_final: 0.8289 (mpp) REVERT: B 296 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.6805 (mp) REVERT: C 33 ASP cc_start: 0.8653 (p0) cc_final: 0.8422 (p0) REVERT: C 56 GLU cc_start: 0.7768 (mp0) cc_final: 0.7171 (mp0) REVERT: C 120 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 130 GLU cc_start: 0.8402 (tt0) cc_final: 0.8090 (tt0) REVERT: C 203 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7453 (p90) REVERT: C 634 LYS cc_start: 0.8297 (pmtt) cc_final: 0.8087 (mmtt) REVERT: C 650 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: C 657 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8506 (pp) REVERT: C 666 PHE cc_start: 0.8393 (t80) cc_final: 0.7681 (t80) REVERT: C 722 ASP cc_start: 0.7300 (t0) cc_final: 0.7048 (t0) REVERT: F 130 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7325 (tm-30) REVERT: F 237 LEU cc_start: 0.9099 (mt) cc_final: 0.8840 (mt) REVERT: F 515 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8904 (tt) REVERT: F 604 ARG cc_start: 0.8029 (tmm-80) cc_final: 0.7765 (ttp80) REVERT: F 648 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: F 656 SER cc_start: 0.8735 (m) cc_final: 0.8459 (p) REVERT: F 687 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: F 722 ASP cc_start: 0.8166 (m-30) cc_final: 0.7742 (p0) REVERT: F 733 ASP cc_start: 0.8081 (m-30) cc_final: 0.7836 (t0) REVERT: F 830 GLU cc_start: 0.7743 (mp0) cc_final: 0.7382 (mp0) REVERT: G 32 GLU cc_start: 0.8364 (pp20) cc_final: 0.8136 (pp20) REVERT: G 67 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7838 (tp30) REVERT: G 130 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7495 (tm-30) REVERT: G 237 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8821 (tp) REVERT: G 266 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: G 405 GLN cc_start: 0.7962 (tt0) cc_final: 0.7698 (tp40) REVERT: G 443 GLU cc_start: 0.8657 (pp20) cc_final: 0.8171 (pp20) REVERT: G 497 ASP cc_start: 0.8262 (t70) cc_final: 0.7891 (t70) REVERT: G 511 ASN cc_start: 0.8321 (t0) cc_final: 0.7883 (t0) REVERT: G 546 LYS cc_start: 0.7981 (tptp) cc_final: 0.7640 (mmtt) REVERT: G 567 SER cc_start: 0.8707 (m) cc_final: 0.8468 (p) REVERT: G 640 ASP cc_start: 0.8431 (t0) cc_final: 0.8057 (t0) REVERT: G 763 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8700 (pp) REVERT: G 779 MET cc_start: 0.7573 (mmt) cc_final: 0.7182 (pmm) REVERT: L 33 ASP cc_start: 0.8221 (p0) cc_final: 0.7965 (p0) REVERT: L 71 GLU cc_start: 0.8594 (tp30) cc_final: 0.8391 (tp30) REVERT: L 172 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: L 203 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7670 (p90) REVERT: L 389 GLU cc_start: 0.7243 (mp0) cc_final: 0.6298 (mp0) REVERT: L 401 MET cc_start: 0.8204 (mmp) cc_final: 0.7655 (mmt) REVERT: L 497 ASP cc_start: 0.8459 (t70) cc_final: 0.8253 (t0) REVERT: L 666 PHE cc_start: 0.8015 (t80) cc_final: 0.7696 (t80) REVERT: L 797 MET cc_start: 0.8451 (ttm) cc_final: 0.8191 (tpp) REVERT: O 71 GLU cc_start: 0.8629 (tp30) cc_final: 0.8293 (tp30) REVERT: O 116 GLN cc_start: 0.9006 (tt0) cc_final: 0.8641 (tt0) REVERT: O 120 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8262 (mt-10) REVERT: O 417 SER cc_start: 0.9103 (m) cc_final: 0.8761 (p) REVERT: O 521 PHE cc_start: 0.6633 (m-80) cc_final: 0.6111 (m-80) REVERT: O 634 LYS cc_start: 0.8718 (pmtt) cc_final: 0.8486 (ptpp) outliers start: 152 outliers final: 83 residues processed: 616 average time/residue: 0.4555 time to fit residues: 462.1450 Evaluate side-chains 549 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 454 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 805 ASP Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 73 GLU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 172 GLU Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 30 GLN Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 590 CYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 359 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 320 optimal weight: 0.4980 chunk 177 optimal weight: 6.9990 chunk 367 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 386 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 506 ASN L 625 GLN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 435 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 673 ASN O 780 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36683 Z= 0.214 Angle : 0.635 10.839 49582 Z= 0.324 Chirality : 0.045 0.172 5563 Planarity : 0.005 0.099 6283 Dihedral : 7.727 100.847 4998 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.05 % Favored : 89.84 % Rotamer: Outliers : 3.91 % Allowed : 14.90 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.23 % 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: -2.07 (0.13), residues: 4428 helix: -0.04 (0.13), residues: 1779 sheet: -1.32 (0.23), residues: 517 loop : -2.62 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 757 HIS 0.005 0.001 HIS C 597 PHE 0.017 0.001 PHE O 504 TYR 0.025 0.001 TYR A 143 ARG 0.008 0.000 ARG L 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 479 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.7954 (mp0) cc_final: 0.7536 (mp0) REVERT: A 226 LEU cc_start: 0.8229 (mt) cc_final: 0.7837 (mp) REVERT: A 278 ASP cc_start: 0.8738 (m-30) cc_final: 0.8287 (m-30) REVERT: A 359 MET cc_start: 0.7766 (mpp) cc_final: 0.6738 (ptt) REVERT: B 130 PHE cc_start: 0.7700 (m-10) cc_final: 0.7430 (m-10) REVERT: B 171 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 296 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6622 (mp) REVERT: B 301 MET cc_start: 0.7388 (mmm) cc_final: 0.7100 (mmm) REVERT: C 56 GLU cc_start: 0.7865 (mp0) cc_final: 0.7324 (mp0) REVERT: C 116 GLN cc_start: 0.9009 (tt0) cc_final: 0.8437 (tt0) REVERT: C 130 GLU cc_start: 0.8312 (tt0) cc_final: 0.8044 (mt-10) REVERT: C 203 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7349 (p90) REVERT: C 226 GLU cc_start: 0.8463 (mp0) cc_final: 0.8142 (mp0) REVERT: C 401 MET cc_start: 0.8388 (mmm) cc_final: 0.7950 (mmt) REVERT: C 650 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7280 (m-10) REVERT: C 722 ASP cc_start: 0.7322 (t0) cc_final: 0.7045 (t0) REVERT: C 733 ASP cc_start: 0.7810 (m-30) cc_final: 0.7486 (t0) REVERT: F 130 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7772 (tm-30) REVERT: F 237 LEU cc_start: 0.9077 (mt) cc_final: 0.8803 (mt) REVERT: F 641 MET cc_start: 0.8718 (mmt) cc_final: 0.8049 (mmt) REVERT: F 656 SER cc_start: 0.8655 (m) cc_final: 0.8423 (p) REVERT: F 687 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7406 (mtp85) REVERT: F 722 ASP cc_start: 0.8166 (m-30) cc_final: 0.7800 (p0) REVERT: F 733 ASP cc_start: 0.8146 (m-30) cc_final: 0.7889 (t0) REVERT: F 830 GLU cc_start: 0.7672 (mp0) cc_final: 0.7351 (mp0) REVERT: G 32 GLU cc_start: 0.8373 (pp20) cc_final: 0.8150 (pp20) REVERT: G 67 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7826 (tp30) REVERT: G 130 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7508 (tm-30) REVERT: G 237 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8852 (tp) REVERT: G 266 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: G 405 GLN cc_start: 0.7946 (tt0) cc_final: 0.7659 (tp40) REVERT: G 409 ASP cc_start: 0.8300 (m-30) cc_final: 0.7745 (m-30) REVERT: G 443 GLU cc_start: 0.8646 (pp20) cc_final: 0.8145 (pp20) REVERT: G 497 ASP cc_start: 0.8223 (t70) cc_final: 0.7902 (t70) REVERT: G 511 ASN cc_start: 0.8321 (t0) cc_final: 0.7962 (t0) REVERT: G 546 LYS cc_start: 0.8001 (tptp) cc_final: 0.7669 (mmtt) REVERT: G 567 SER cc_start: 0.8723 (m) cc_final: 0.8459 (p) REVERT: G 640 ASP cc_start: 0.8450 (t0) cc_final: 0.8116 (t0) REVERT: G 682 ASN cc_start: 0.8567 (m-40) cc_final: 0.8256 (t0) REVERT: G 763 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8679 (pp) REVERT: G 779 MET cc_start: 0.7497 (mmt) cc_final: 0.7264 (pmm) REVERT: L 33 ASP cc_start: 0.8274 (p0) cc_final: 0.8018 (p0) REVERT: L 172 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: L 203 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7687 (p90) REVERT: L 634 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (pmtt) REVERT: L 666 PHE cc_start: 0.8007 (t80) cc_final: 0.7708 (t80) REVERT: L 797 MET cc_start: 0.8437 (ttm) cc_final: 0.8199 (tpp) REVERT: O 71 GLU cc_start: 0.8631 (tp30) cc_final: 0.8279 (tp30) REVERT: O 116 GLN cc_start: 0.8931 (tt0) cc_final: 0.8613 (tt0) REVERT: O 120 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8266 (mt-10) REVERT: O 417 SER cc_start: 0.9109 (m) cc_final: 0.8770 (p) REVERT: O 521 PHE cc_start: 0.6646 (m-80) cc_final: 0.6073 (m-80) REVERT: O 634 LYS cc_start: 0.8600 (pmtt) cc_final: 0.8379 (ptpp) outliers start: 158 outliers final: 96 residues processed: 589 average time/residue: 0.4589 time to fit residues: 445.5771 Evaluate side-chains 548 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 442 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 703 GLU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 172 GLU Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 335 ASN Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 435 GLN Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 726 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 145 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 431 optimal weight: 0.0980 chunk 358 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 226 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN C 611 ASN ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 HIS ** F 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 GLN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 780 GLN O 335 ASN O 435 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 775 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36683 Z= 0.289 Angle : 0.674 11.955 49582 Z= 0.344 Chirality : 0.047 0.200 5563 Planarity : 0.005 0.099 6283 Dihedral : 7.685 92.532 4998 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.52 % Favored : 89.39 % Rotamer: Outliers : 4.10 % Allowed : 15.27 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 4428 helix: -0.01 (0.13), residues: 1776 sheet: -0.95 (0.24), residues: 502 loop : -2.61 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 757 HIS 0.006 0.001 HIS G 514 PHE 0.035 0.002 PHE G 504 TYR 0.026 0.001 TYR A 143 ARG 0.007 0.001 ARG L 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 445 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8247 (mt) cc_final: 0.7862 (mp) REVERT: A 278 ASP cc_start: 0.8855 (m-30) cc_final: 0.8408 (m-30) REVERT: A 359 MET cc_start: 0.7787 (mpp) cc_final: 0.6762 (ptt) REVERT: B 130 PHE cc_start: 0.7928 (m-10) cc_final: 0.7635 (m-10) REVERT: B 171 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 296 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6752 (mt) REVERT: C 130 GLU cc_start: 0.8477 (tt0) cc_final: 0.8107 (mt-10) REVERT: C 230 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: C 401 MET cc_start: 0.8300 (mmm) cc_final: 0.7976 (mmt) REVERT: C 650 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7360 (m-10) REVERT: C 722 ASP cc_start: 0.7363 (t0) cc_final: 0.6948 (t0) REVERT: C 733 ASP cc_start: 0.7838 (m-30) cc_final: 0.7476 (t0) REVERT: F 130 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 237 LEU cc_start: 0.9164 (mt) cc_final: 0.8847 (mt) REVERT: F 545 ASN cc_start: 0.6756 (m-40) cc_final: 0.6302 (m-40) REVERT: F 641 MET cc_start: 0.8686 (mmt) cc_final: 0.8011 (mmt) REVERT: F 656 SER cc_start: 0.8685 (m) cc_final: 0.8461 (p) REVERT: F 687 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7518 (mtp85) REVERT: F 830 GLU cc_start: 0.7836 (mp0) cc_final: 0.7570 (mp0) REVERT: G 32 GLU cc_start: 0.8399 (pp20) cc_final: 0.8139 (pp20) REVERT: G 67 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7824 (tp30) REVERT: G 71 GLU cc_start: 0.7818 (tp30) cc_final: 0.7514 (tp30) REVERT: G 130 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7555 (tm-30) REVERT: G 266 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: G 405 GLN cc_start: 0.8180 (tt0) cc_final: 0.7740 (tp40) REVERT: G 434 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8112 (tp-100) REVERT: G 443 GLU cc_start: 0.8665 (pp20) cc_final: 0.8124 (pp20) REVERT: G 497 ASP cc_start: 0.8136 (t70) cc_final: 0.7801 (t0) REVERT: G 511 ASN cc_start: 0.8432 (t0) cc_final: 0.8007 (t0) REVERT: G 546 LYS cc_start: 0.8000 (tptp) cc_final: 0.7656 (mmtt) REVERT: G 567 SER cc_start: 0.8839 (m) cc_final: 0.8559 (p) REVERT: G 640 ASP cc_start: 0.8552 (t0) cc_final: 0.8234 (t0) REVERT: G 682 ASN cc_start: 0.8531 (m-40) cc_final: 0.8241 (t0) REVERT: G 763 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8686 (pp) REVERT: G 779 MET cc_start: 0.7706 (mmt) cc_final: 0.7375 (pmm) REVERT: L 33 ASP cc_start: 0.8282 (p0) cc_final: 0.7970 (p0) REVERT: L 203 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7551 (p90) REVERT: L 401 MET cc_start: 0.8077 (mmp) cc_final: 0.7535 (mmt) REVERT: L 634 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7921 (pmtt) REVERT: L 650 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.6639 (t80) REVERT: L 797 MET cc_start: 0.8458 (ttm) cc_final: 0.8255 (tpp) REVERT: O 71 GLU cc_start: 0.8619 (tp30) cc_final: 0.8268 (tp30) REVERT: O 116 GLN cc_start: 0.9039 (tt0) cc_final: 0.8615 (tt0) REVERT: O 120 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8224 (mt-10) REVERT: O 336 ASP cc_start: 0.8677 (m-30) cc_final: 0.8473 (p0) REVERT: O 417 SER cc_start: 0.9172 (m) cc_final: 0.8844 (p) REVERT: O 521 PHE cc_start: 0.6498 (m-80) cc_final: 0.6006 (m-80) REVERT: O 634 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8336 (ptpp) outliers start: 166 outliers final: 106 residues processed: 567 average time/residue: 0.4668 time to fit residues: 435.3861 Evaluate side-chains 542 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 426 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 703 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 335 ASN Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 743 GLU Chi-restraints excluded: chain L residue 744 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 726 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 416 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 363 optimal weight: 0.9990 chunk 240 optimal weight: 0.0570 chunk 429 optimal weight: 0.4980 chunk 269 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 506 ASN L 625 GLN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 812 GLN O 435 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36683 Z= 0.175 Angle : 0.632 11.777 49582 Z= 0.319 Chirality : 0.044 0.245 5563 Planarity : 0.004 0.096 6283 Dihedral : 7.232 87.149 4998 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 3.44 % Allowed : 16.11 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 4428 helix: 0.20 (0.13), residues: 1768 sheet: -1.22 (0.24), residues: 507 loop : -2.49 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 757 HIS 0.004 0.001 HIS C 597 PHE 0.022 0.001 PHE G 504 TYR 0.025 0.001 TYR A 143 ARG 0.007 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 502 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8279 (mt) cc_final: 0.7843 (mp) REVERT: A 278 ASP cc_start: 0.8779 (m-30) cc_final: 0.8372 (m-30) REVERT: B 130 PHE cc_start: 0.7668 (m-10) cc_final: 0.7340 (m-10) REVERT: B 171 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7312 (mt-10) REVERT: B 296 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6838 (mp) REVERT: C 116 GLN cc_start: 0.8953 (tt0) cc_final: 0.8430 (tt0) REVERT: C 120 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7856 (mm-30) REVERT: C 130 GLU cc_start: 0.8403 (tt0) cc_final: 0.7981 (mt-10) REVERT: C 203 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7138 (p90) REVERT: C 401 MET cc_start: 0.8248 (mmm) cc_final: 0.7920 (mmt) REVERT: C 514 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8322 (p-80) REVERT: C 622 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8062 (p0) REVERT: C 650 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: C 722 ASP cc_start: 0.7250 (t0) cc_final: 0.6840 (t0) REVERT: C 733 ASP cc_start: 0.7764 (m-30) cc_final: 0.7402 (t0) REVERT: F 130 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7785 (tm-30) REVERT: F 237 LEU cc_start: 0.9078 (mt) cc_final: 0.8794 (mt) REVERT: F 545 ASN cc_start: 0.6766 (m-40) cc_final: 0.6275 (m110) REVERT: F 641 MET cc_start: 0.8583 (mmt) cc_final: 0.8060 (mmt) REVERT: F 656 SER cc_start: 0.8631 (m) cc_final: 0.8383 (p) REVERT: F 687 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7298 (mtp85) REVERT: F 733 ASP cc_start: 0.7995 (m-30) cc_final: 0.7602 (t0) REVERT: F 805 ASP cc_start: 0.7199 (m-30) cc_final: 0.6688 (p0) REVERT: F 830 GLU cc_start: 0.7702 (mp0) cc_final: 0.7387 (mp0) REVERT: G 32 GLU cc_start: 0.8367 (pp20) cc_final: 0.8114 (pp20) REVERT: G 67 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7785 (tp30) REVERT: G 71 GLU cc_start: 0.7859 (tp30) cc_final: 0.7565 (tp30) REVERT: G 124 LYS cc_start: 0.8993 (tmmt) cc_final: 0.8593 (tptp) REVERT: G 130 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7509 (tm-30) REVERT: G 266 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: G 405 GLN cc_start: 0.7972 (tt0) cc_final: 0.7608 (tp40) REVERT: G 434 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8045 (tp-100) REVERT: G 443 GLU cc_start: 0.8601 (pp20) cc_final: 0.8118 (pp20) REVERT: G 497 ASP cc_start: 0.8111 (t70) cc_final: 0.7883 (t70) REVERT: G 511 ASN cc_start: 0.8306 (t0) cc_final: 0.7918 (t0) REVERT: G 546 LYS cc_start: 0.7945 (tptp) cc_final: 0.7626 (mmtt) REVERT: G 567 SER cc_start: 0.8744 (m) cc_final: 0.8494 (p) REVERT: G 640 ASP cc_start: 0.8638 (t0) cc_final: 0.8342 (t0) REVERT: G 682 ASN cc_start: 0.8536 (m-40) cc_final: 0.8295 (t0) REVERT: G 763 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8665 (pp) REVERT: G 779 MET cc_start: 0.7674 (mmt) cc_final: 0.7371 (pmm) REVERT: G 819 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7861 (ptp-110) REVERT: L 203 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7532 (p90) REVERT: L 374 HIS cc_start: 0.8300 (m-70) cc_final: 0.8027 (m170) REVERT: L 401 MET cc_start: 0.7996 (mmp) cc_final: 0.7335 (mmt) REVERT: L 434 GLN cc_start: 0.8358 (tp-100) cc_final: 0.7966 (tp-100) REVERT: L 602 PHE cc_start: 0.7842 (p90) cc_final: 0.7040 (p90) REVERT: L 634 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (pmtt) REVERT: L 650 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6441 (t80) REVERT: L 663 LEU cc_start: 0.9039 (tp) cc_final: 0.8697 (tt) REVERT: O 71 GLU cc_start: 0.8621 (tp30) cc_final: 0.8265 (tp30) REVERT: O 116 GLN cc_start: 0.9023 (tt0) cc_final: 0.8671 (tt0) REVERT: O 120 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8212 (mt-10) REVERT: O 336 ASP cc_start: 0.8669 (m-30) cc_final: 0.8458 (p0) REVERT: O 417 SER cc_start: 0.9096 (m) cc_final: 0.8783 (p) REVERT: O 443 GLU cc_start: 0.8845 (pp20) cc_final: 0.8299 (pp20) REVERT: O 490 MET cc_start: 0.8442 (mmm) cc_final: 0.8191 (tpp) REVERT: O 521 PHE cc_start: 0.6455 (m-80) cc_final: 0.5979 (m-80) REVERT: O 634 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8334 (ptpp) outliers start: 139 outliers final: 93 residues processed: 603 average time/residue: 0.4674 time to fit residues: 463.4274 Evaluate side-chains 567 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 462 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 703 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 335 ASN Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 743 GLU Chi-restraints excluded: chain L residue 763 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 265 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN G 611 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 GLN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36683 Z= 0.338 Angle : 0.713 13.859 49582 Z= 0.363 Chirality : 0.048 0.200 5563 Planarity : 0.005 0.098 6283 Dihedral : 7.553 83.141 4998 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.14 % Rotamer: Outliers : 3.61 % Allowed : 16.56 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.90 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4428 helix: 0.05 (0.13), residues: 1771 sheet: -0.89 (0.24), residues: 502 loop : -2.50 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP O 448 HIS 0.005 0.001 HIS B 196 PHE 0.024 0.002 PHE G 504 TYR 0.025 0.002 TYR A 143 ARG 0.009 0.001 ARG F 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 445 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8317 (mt) cc_final: 0.7903 (mp) REVERT: A 278 ASP cc_start: 0.8944 (m-30) cc_final: 0.8455 (m-30) REVERT: B 107 ASP cc_start: 0.8513 (t70) cc_final: 0.7950 (t0) REVERT: B 130 PHE cc_start: 0.8095 (m-10) cc_final: 0.7730 (m-10) REVERT: B 171 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7514 (mt-10) REVERT: B 296 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7131 (mp) REVERT: C 56 GLU cc_start: 0.7968 (mp0) cc_final: 0.7336 (mp0) REVERT: C 120 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 130 GLU cc_start: 0.8524 (tt0) cc_final: 0.8254 (tt0) REVERT: C 401 MET cc_start: 0.8281 (mmm) cc_final: 0.8035 (mmt) REVERT: C 497 ASP cc_start: 0.8624 (t70) cc_final: 0.8390 (t0) REVERT: C 622 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.7892 (p0) REVERT: C 650 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: C 722 ASP cc_start: 0.7430 (t0) cc_final: 0.6995 (t0) REVERT: C 732 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9015 (mm) REVERT: C 733 ASP cc_start: 0.7806 (m-30) cc_final: 0.7489 (t0) REVERT: F 130 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7797 (tm-30) REVERT: F 545 ASN cc_start: 0.6896 (m-40) cc_final: 0.6423 (m-40) REVERT: F 623 LEU cc_start: 0.8718 (mt) cc_final: 0.8423 (tt) REVERT: F 641 MET cc_start: 0.8637 (mmt) cc_final: 0.7991 (mmt) REVERT: F 656 SER cc_start: 0.8583 (m) cc_final: 0.8367 (p) REVERT: F 687 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7465 (mtp85) REVERT: F 733 ASP cc_start: 0.8123 (m-30) cc_final: 0.7715 (t0) REVERT: G 32 GLU cc_start: 0.8399 (pp20) cc_final: 0.8123 (pp20) REVERT: G 67 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7805 (tp30) REVERT: G 71 GLU cc_start: 0.7851 (tp30) cc_final: 0.7536 (tp30) REVERT: G 130 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7609 (tm-30) REVERT: G 266 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: G 434 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8091 (tp-100) REVERT: G 443 GLU cc_start: 0.8660 (pp20) cc_final: 0.8048 (pp20) REVERT: G 497 ASP cc_start: 0.8074 (t70) cc_final: 0.7802 (t0) REVERT: G 511 ASN cc_start: 0.8476 (t0) cc_final: 0.8079 (t0) REVERT: G 543 GLU cc_start: 0.8213 (mp0) cc_final: 0.7949 (mp0) REVERT: G 546 LYS cc_start: 0.7838 (tptp) cc_final: 0.7540 (mmtt) REVERT: G 567 SER cc_start: 0.8818 (m) cc_final: 0.8559 (p) REVERT: G 625 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6575 (pp30) REVERT: G 640 ASP cc_start: 0.8582 (t0) cc_final: 0.8307 (t0) REVERT: G 682 ASN cc_start: 0.8505 (m-40) cc_final: 0.8239 (t0) REVERT: G 763 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8716 (pp) REVERT: G 779 MET cc_start: 0.7817 (mmt) cc_final: 0.7417 (pmm) REVERT: L 28 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7686 (ptp-170) REVERT: L 203 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7503 (p90) REVERT: L 602 PHE cc_start: 0.7943 (p90) cc_final: 0.7173 (p90) REVERT: L 634 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7939 (pmtt) REVERT: L 650 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6476 (t80) REVERT: L 797 MET cc_start: 0.8428 (tpp) cc_final: 0.8087 (tpp) REVERT: O 120 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8174 (mt-10) REVERT: O 279 LYS cc_start: 0.9023 (mttt) cc_final: 0.8664 (ttmm) REVERT: O 336 ASP cc_start: 0.8761 (m-30) cc_final: 0.8540 (p0) REVERT: O 417 SER cc_start: 0.9193 (m) cc_final: 0.8865 (p) REVERT: O 521 PHE cc_start: 0.6450 (m-80) cc_final: 0.5961 (m-80) REVERT: O 634 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8391 (pttm) REVERT: O 744 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8745 (pt) outliers start: 146 outliers final: 112 residues processed: 550 average time/residue: 0.4585 time to fit residues: 416.3571 Evaluate side-chains 545 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 420 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 335 ASN Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 743 GLU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 726 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 391 optimal weight: 3.9990 chunk 411 optimal weight: 0.8980 chunk 375 optimal weight: 0.8980 chunk 400 optimal weight: 0.0870 chunk 241 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 361 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 399 optimal weight: 0.0970 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN C 611 ASN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 GLN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36683 Z= 0.175 Angle : 0.654 15.288 49582 Z= 0.329 Chirality : 0.045 0.211 5563 Planarity : 0.005 0.097 6283 Dihedral : 7.117 80.428 4998 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 3.14 % Allowed : 17.20 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 4428 helix: 0.28 (0.13), residues: 1769 sheet: -1.03 (0.24), residues: 492 loop : -2.40 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 757 HIS 0.004 0.001 HIS L 157 PHE 0.016 0.001 PHE G 504 TYR 0.023 0.001 TYR A 143 ARG 0.008 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 482 time to evaluate : 4.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8211 (mt) cc_final: 0.7848 (mp) REVERT: A 278 ASP cc_start: 0.8750 (m-30) cc_final: 0.8313 (m-30) REVERT: B 107 ASP cc_start: 0.8431 (t70) cc_final: 0.7847 (t0) REVERT: B 171 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7400 (mt-10) REVERT: B 296 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7056 (mp) REVERT: C 28 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7787 (ttm110) REVERT: C 56 GLU cc_start: 0.7899 (mp0) cc_final: 0.7359 (mp0) REVERT: C 71 GLU cc_start: 0.8923 (tp30) cc_final: 0.8703 (tp30) REVERT: C 116 GLN cc_start: 0.8988 (tt0) cc_final: 0.8412 (tt0) REVERT: C 120 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 130 GLU cc_start: 0.8368 (tt0) cc_final: 0.8021 (mt-10) REVERT: C 203 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7038 (p90) REVERT: C 401 MET cc_start: 0.8170 (mmm) cc_final: 0.7879 (mmt) REVERT: C 622 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8157 (p0) REVERT: C 722 ASP cc_start: 0.7178 (t0) cc_final: 0.6783 (t0) REVERT: C 733 ASP cc_start: 0.7833 (m-30) cc_final: 0.7552 (t0) REVERT: F 130 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7812 (tm-30) REVERT: F 237 LEU cc_start: 0.9101 (mt) cc_final: 0.8800 (mt) REVERT: F 545 ASN cc_start: 0.6829 (m-40) cc_final: 0.6318 (m110) REVERT: F 640 ASP cc_start: 0.8341 (t0) cc_final: 0.7903 (t0) REVERT: F 641 MET cc_start: 0.8531 (mmt) cc_final: 0.8091 (mmt) REVERT: F 656 SER cc_start: 0.8631 (m) cc_final: 0.8428 (p) REVERT: F 687 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7361 (mtp85) REVERT: F 733 ASP cc_start: 0.7998 (m-30) cc_final: 0.7547 (t0) REVERT: F 830 GLU cc_start: 0.7700 (mp0) cc_final: 0.7475 (mp0) REVERT: G 32 GLU cc_start: 0.8379 (pp20) cc_final: 0.8120 (pp20) REVERT: G 67 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7784 (tp30) REVERT: G 71 GLU cc_start: 0.7877 (tp30) cc_final: 0.7514 (tp30) REVERT: G 130 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7513 (tm-30) REVERT: G 405 GLN cc_start: 0.8174 (tt0) cc_final: 0.7694 (tp40) REVERT: G 434 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8090 (tp-100) REVERT: G 443 GLU cc_start: 0.8580 (pp20) cc_final: 0.8102 (pp20) REVERT: G 511 ASN cc_start: 0.8392 (t0) cc_final: 0.7997 (t0) REVERT: G 543 GLU cc_start: 0.8294 (mp0) cc_final: 0.7994 (mp0) REVERT: G 546 LYS cc_start: 0.7789 (tptp) cc_final: 0.7500 (mmtt) REVERT: G 567 SER cc_start: 0.8729 (m) cc_final: 0.8467 (p) REVERT: G 625 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6597 (pp30) REVERT: G 640 ASP cc_start: 0.8566 (t0) cc_final: 0.8329 (t0) REVERT: G 682 ASN cc_start: 0.8469 (m-40) cc_final: 0.8258 (t0) REVERT: G 763 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8700 (pp) REVERT: G 779 MET cc_start: 0.7742 (mmt) cc_final: 0.7462 (pmm) REVERT: L 28 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7615 (ptp-170) REVERT: L 203 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7399 (p90) REVERT: L 374 HIS cc_start: 0.8337 (m-70) cc_final: 0.8096 (m170) REVERT: L 401 MET cc_start: 0.7807 (mmp) cc_final: 0.7248 (mmt) REVERT: L 434 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8117 (tp-100) REVERT: L 602 PHE cc_start: 0.7813 (p90) cc_final: 0.7113 (p90) REVERT: L 634 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7929 (pmtt) REVERT: L 663 LEU cc_start: 0.9041 (tp) cc_final: 0.8713 (tt) REVERT: L 797 MET cc_start: 0.8478 (tpp) cc_final: 0.8192 (tpp) REVERT: O 116 GLN cc_start: 0.8984 (tt0) cc_final: 0.8633 (tt0) REVERT: O 120 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8208 (mt-10) REVERT: O 279 LYS cc_start: 0.9055 (mttt) cc_final: 0.8678 (ttmm) REVERT: O 336 ASP cc_start: 0.8700 (m-30) cc_final: 0.8491 (p0) REVERT: O 417 SER cc_start: 0.9066 (m) cc_final: 0.8748 (p) REVERT: O 490 MET cc_start: 0.8409 (mmm) cc_final: 0.8199 (tpp) REVERT: O 521 PHE cc_start: 0.6429 (m-80) cc_final: 0.5965 (m-80) REVERT: O 744 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8714 (pt) outliers start: 127 outliers final: 98 residues processed: 574 average time/residue: 0.4711 time to fit residues: 440.7119 Evaluate side-chains 560 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 453 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 634 LYS Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 335 ASN Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 614 ILE Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 726 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 263 optimal weight: 0.7980 chunk 423 optimal weight: 0.8980 chunk 258 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 chunk 444 optimal weight: 0.9980 chunk 408 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 273 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 335 ASN ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 GLN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 780 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36683 Z= 0.182 Angle : 0.657 15.149 49582 Z= 0.328 Chirality : 0.045 0.214 5563 Planarity : 0.005 0.095 6283 Dihedral : 7.009 82.187 4998 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.03 % Favored : 89.95 % Rotamer: Outliers : 2.64 % Allowed : 17.87 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 4428 helix: 0.31 (0.13), residues: 1769 sheet: -1.20 (0.23), residues: 507 loop : -2.32 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP L 757 HIS 0.004 0.001 HIS L 157 PHE 0.026 0.001 PHE L 666 TYR 0.022 0.001 TYR A 143 ARG 0.009 0.000 ARG F 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 477 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.6809 (mmp) cc_final: 0.6559 (tpp) REVERT: A 220 PHE cc_start: 0.8037 (t80) cc_final: 0.7632 (t80) REVERT: A 226 LEU cc_start: 0.8258 (mt) cc_final: 0.7875 (mp) REVERT: A 278 ASP cc_start: 0.8715 (m-30) cc_final: 0.8229 (m-30) REVERT: B 107 ASP cc_start: 0.8370 (t70) cc_final: 0.8075 (t0) REVERT: B 171 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7424 (mt-10) REVERT: B 296 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7181 (mp) REVERT: C 56 GLU cc_start: 0.7952 (mp0) cc_final: 0.7441 (mp0) REVERT: C 71 GLU cc_start: 0.8912 (tp30) cc_final: 0.8678 (tp30) REVERT: C 116 GLN cc_start: 0.8991 (tt0) cc_final: 0.8376 (tt0) REVERT: C 120 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7952 (mm-30) REVERT: C 130 GLU cc_start: 0.8377 (tt0) cc_final: 0.8024 (mt-10) REVERT: C 203 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7070 (p90) REVERT: C 235 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6890 (mtt180) REVERT: C 401 MET cc_start: 0.8174 (mmm) cc_final: 0.7884 (mmt) REVERT: C 514 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8298 (p-80) REVERT: C 722 ASP cc_start: 0.7244 (t0) cc_final: 0.6846 (t0) REVERT: C 733 ASP cc_start: 0.7791 (m-30) cc_final: 0.7500 (t0) REVERT: F 130 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7858 (tm-30) REVERT: F 237 LEU cc_start: 0.9117 (mt) cc_final: 0.8802 (mt) REVERT: F 545 ASN cc_start: 0.6797 (m-40) cc_final: 0.6283 (m-40) REVERT: F 641 MET cc_start: 0.8435 (mmt) cc_final: 0.7979 (mmt) REVERT: F 687 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7392 (mtp85) REVERT: F 733 ASP cc_start: 0.8019 (m-30) cc_final: 0.7576 (t0) REVERT: F 830 GLU cc_start: 0.7646 (mp0) cc_final: 0.7368 (mp0) REVERT: G 32 GLU cc_start: 0.8433 (pp20) cc_final: 0.8137 (pp20) REVERT: G 67 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7771 (tp30) REVERT: G 71 GLU cc_start: 0.7884 (tp30) cc_final: 0.7530 (tp30) REVERT: G 130 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7521 (tm-30) REVERT: G 434 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8079 (tp-100) REVERT: G 443 GLU cc_start: 0.8539 (pp20) cc_final: 0.8072 (pp20) REVERT: G 511 ASN cc_start: 0.8326 (t0) cc_final: 0.7949 (t0) REVERT: G 543 GLU cc_start: 0.8307 (mp0) cc_final: 0.8031 (mp0) REVERT: G 546 LYS cc_start: 0.7794 (tptp) cc_final: 0.7507 (mmtt) REVERT: G 567 SER cc_start: 0.8717 (m) cc_final: 0.8477 (p) REVERT: G 625 GLN cc_start: 0.7153 (tm-30) cc_final: 0.6598 (pp30) REVERT: G 640 ASP cc_start: 0.8605 (t0) cc_final: 0.8335 (t0) REVERT: G 682 ASN cc_start: 0.8468 (m-40) cc_final: 0.8267 (t0) REVERT: G 763 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8667 (pp) REVERT: G 779 MET cc_start: 0.7708 (mmt) cc_final: 0.7448 (pmm) REVERT: L 28 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7620 (ptp-170) REVERT: L 203 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7548 (p90) REVERT: L 374 HIS cc_start: 0.8337 (m-70) cc_final: 0.8080 (m170) REVERT: L 401 MET cc_start: 0.7761 (mmp) cc_final: 0.7180 (mmt) REVERT: L 434 GLN cc_start: 0.8447 (tp-100) cc_final: 0.8181 (tp-100) REVERT: L 602 PHE cc_start: 0.7796 (p90) cc_final: 0.6974 (p90) REVERT: L 634 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7933 (pmtt) REVERT: L 663 LEU cc_start: 0.9001 (tp) cc_final: 0.8657 (tt) REVERT: L 797 MET cc_start: 0.8497 (tpp) cc_final: 0.8211 (tpp) REVERT: O 116 GLN cc_start: 0.8993 (tt0) cc_final: 0.8622 (tt0) REVERT: O 120 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8208 (mt-10) REVERT: O 279 LYS cc_start: 0.9019 (mttt) cc_final: 0.8668 (ttmm) REVERT: O 417 SER cc_start: 0.9111 (m) cc_final: 0.8793 (p) REVERT: O 443 GLU cc_start: 0.8837 (pp20) cc_final: 0.8253 (pp20) REVERT: O 521 PHE cc_start: 0.6409 (m-80) cc_final: 0.5937 (m-80) outliers start: 107 outliers final: 93 residues processed: 561 average time/residue: 0.4516 time to fit residues: 419.4409 Evaluate side-chains 549 residues out of total 4046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 448 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 634 LYS Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 614 ILE Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 281 optimal weight: 0.2980 chunk 376 optimal weight: 0.6980 chunk 108 optimal weight: 0.0980 chunk 326 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 chunk 354 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078965 restraints weight = 89490.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081547 restraints weight = 50974.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083236 restraints weight = 35513.206| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36683 Z= 0.163 Angle : 0.651 15.089 49582 Z= 0.324 Chirality : 0.044 0.223 5563 Planarity : 0.005 0.095 6283 Dihedral : 6.841 82.100 4998 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.08 % Favored : 90.90 % Rotamer: Outliers : 2.55 % Allowed : 18.44 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 4428 helix: 0.41 (0.13), residues: 1758 sheet: -1.17 (0.24), residues: 505 loop : -2.24 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP L 757 HIS 0.004 0.001 HIS L 157 PHE 0.019 0.001 PHE C 650 TYR 0.017 0.001 TYR A 143 ARG 0.009 0.000 ARG G 670 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8565.24 seconds wall clock time: 156 minutes 14.74 seconds (9374.74 seconds total)