Starting phenix.real_space_refine on Tue Feb 13 04:18:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/02_2024/6j5t_0680_updated.pdb" } resolution = 3.4 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= 0.003 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 25 5.49 5 S 310 5.16 5 C 33970 2.51 5 N 9145 2.21 5 O 10038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 190": "NH1" <-> "NH2" Residue "H PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 326": "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 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 670": "NH1" <-> "NH2" Residue "G ARG 840": "NH1" <-> "NH2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "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 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 670": "NH1" <-> "NH2" Residue "C ARG 840": "NH1" <-> "NH2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 326": "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 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 670": "NH1" <-> "NH2" Residue "F ARG 840": "NH1" <-> "NH2" Residue "J TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 190": "NH1" <-> "NH2" Residue "K PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 326": "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 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 670": "NH1" <-> "NH2" Residue "L ARG 840": "NH1" <-> "NH2" Residue "M TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 326": "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 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 670": "NH1" <-> "NH2" Residue "O ARG 840": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 53488 Number of models: 1 Model: "" Number of chains: 25 Chain: "I" 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: "H" 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: "G" Number of atoms: 6476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6476 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 27, 'TRANS': 780} Chain breaks: 2 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: 6476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6476 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 27, 'TRANS': 780} Chain breaks: 2 Chain: "D" 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: "E" 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: "F" Number of atoms: 6476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6476 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 27, 'TRANS': 780} Chain breaks: 2 Chain: "J" 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: "K" 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: "L" Number of atoms: 6476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6476 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 27, 'TRANS': 780} Chain breaks: 2 Chain: "M" 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: "N" 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: "O" Number of atoms: 6476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6476 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 27, 'TRANS': 780} Chain breaks: 2 Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 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: "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: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 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: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 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: "M" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 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: 5 residue: pdb=" N BQL I 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL I 501 " occ=0.00 residue: pdb=" N BQL A 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL A 501 " occ=0.00 residue: pdb=" N BQL D 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL D 501 " occ=0.00 residue: pdb=" N BQL J 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL J 501 " occ=0.00 residue: pdb=" N BQL M 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL M 501 " occ=0.00 Time building chain proxies: 19.92, per 1000 atoms: 0.37 Number of scatterers: 53488 At special positions: 0 Unit cell: (245.475, 241.111, 124.374, 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 310 16.00 P 25 15.00 O 10038 8.00 N 9145 7.00 C 33970 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=10, symmetry=0 Simple link: pdb=" C VAL A 252 " - pdb=" N BQL A 501 " Simple link: pdb=" C VAL D 252 " - pdb=" N BQL D 501 " Simple link: pdb=" C VAL I 252 " - pdb=" N BQL I 501 " Simple link: pdb=" C VAL J 252 " - pdb=" N BQL J 501 " Simple link: pdb=" C VAL M 252 " - pdb=" N BQL M 501 " Simple link: pdb=" N LYS A 255 " - pdb=" C BQO A 502 " Simple link: pdb=" N LYS D 255 " - pdb=" C BQO D 502 " Simple link: pdb=" N LYS I 255 " - pdb=" C BQO I 502 " Simple link: pdb=" N LYS J 255 " - pdb=" C BQO J 502 " Simple link: pdb=" N LYS M 255 " - pdb=" C BQO M 502 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.17 Conformation dependent library (CDL) restraints added in 7.0 seconds 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12490 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 242 helices and 30 sheets defined 38.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.38 Creating SS restraints... Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 194 through 210 Processing helix chain 'I' and resid 265 through 269 Processing helix chain 'I' and resid 276 through 291 Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 359 through 366 removed outlier: 3.622A pdb=" N LEU I 366 " --> pdb=" O VAL I 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 38 removed outlier: 3.814A pdb=" N ASN H 26 " --> pdb=" O TRP H 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER H 28 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 56 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 102 through 116 removed outlier: 3.945A pdb=" N SER H 115 " --> pdb=" O SER H 111 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 181 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 247 through 263 removed outlier: 5.341A pdb=" N TYR H 252 " --> pdb=" O THR H 249 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 263 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 288 Processing helix chain 'H' and resid 308 through 322 Processing helix chain 'H' and resid 333 through 346 Processing helix chain 'G' and resid 7 through 48 removed outlier: 3.818A pdb=" N VAL G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 75 removed outlier: 3.850A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'G' and resid 109 through 135 Proline residue: G 131 - end of helix Processing helix chain 'G' and resid 164 through 176 removed outlier: 3.962A pdb=" N ARG G 176 " --> pdb=" O GLU G 172 " (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 237 Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.659A pdb=" N LEU G 250 " --> pdb=" O ILE G 246 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG G 251 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 255 " --> pdb=" O ARG G 251 " (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 345 through 355 Processing helix chain 'G' and resid 359 through 370 Processing helix chain 'G' and resid 376 through 384 Processing helix chain 'G' and resid 386 through 396 removed outlier: 6.796A pdb=" N THR G 394 " --> pdb=" O LEU G 390 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER G 395 " --> pdb=" O ARG G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 408 removed outlier: 3.874A pdb=" N SER G 407 " --> pdb=" O SER G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 422 removed outlier: 3.708A pdb=" N THR G 421 " --> pdb=" O SER G 417 " (cutoff:3.500A) removed outlier: 4.338A 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 467 Processing helix chain 'G' and resid 489 through 500 Processing helix chain 'G' and resid 549 through 556 removed outlier: 3.813A pdb=" N THR G 556 " --> pdb=" O ALA G 552 " (cutoff:3.500A) 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 605 through 608 removed outlier: 3.747A pdb=" N ASP G 608 " --> pdb=" O SER G 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 605 through 608' Processing helix chain 'G' and resid 628 through 631 Processing helix chain 'G' and resid 653 through 655 No H-bonds generated for 'chain 'G' and resid 653 through 655' Processing helix chain 'G' and resid 678 through 682 removed outlier: 3.551A pdb=" N LYS G 681 " --> pdb=" O SER G 678 " (cutoff:3.500A) 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 732 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 808 through 814 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.614A pdb=" N LEU A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.814A pdb=" N ASN B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.945A pdb=" N SER B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 4.832A 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 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 247 through 263 removed outlier: 5.340A pdb=" N TYR B 252 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.908A 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 322 Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'C' and resid 7 through 48 removed outlier: 3.818A pdb=" N VAL C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ARG C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 75 removed outlier: 3.850A pdb=" N GLU C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 109 through 135 Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.962A pdb=" N ARG C 176 " --> pdb=" O GLU C 172 " (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 237 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.659A pdb=" N LEU C 250 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 255 " --> pdb=" O ARG C 251 " (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 345 through 355 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 386 through 396 removed outlier: 6.796A pdb=" N THR C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 removed outlier: 3.875A pdb=" N SER C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.706A pdb=" N THR C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 4.339A 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 467 Processing helix chain 'C' and resid 489 through 500 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 605 through 608 removed outlier: 3.747A pdb=" N ASP C 608 " --> pdb=" O SER C 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 628 through 631 Processing helix chain 'C' and resid 653 through 655 No H-bonds generated for 'chain 'C' and resid 653 through 655' Processing helix chain 'C' and resid 678 through 682 removed outlier: 3.552A pdb=" N LYS C 681 " --> pdb=" O SER C 678 " (cutoff:3.500A) 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 732 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 808 through 814 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 194 through 210 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 276 through 291 Processing helix chain 'D' and resid 332 through 335 removed outlier: 4.380A pdb=" N GLN D 335 " --> pdb=" O GLN D 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.563A pdb=" N LEU D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 38 removed outlier: 3.814A pdb=" N ASN E 26 " --> pdb=" O TRP E 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.945A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 181 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 247 through 263 removed outlier: 5.340A pdb=" N TYR E 252 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR E 263 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 288 Processing helix chain 'E' and resid 308 through 322 Processing helix chain 'E' and resid 333 through 346 Processing helix chain 'F' and resid 7 through 48 removed outlier: 3.818A pdb=" N VAL F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS F 29 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 75 removed outlier: 3.851A pdb=" N GLU F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 109 through 135 Proline residue: F 131 - end of helix Processing helix chain 'F' and resid 164 through 176 removed outlier: 3.963A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (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 237 Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.658A pdb=" N LEU F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG F 251 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F 255 " --> pdb=" O ARG F 251 " (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 345 through 355 Processing helix chain 'F' and resid 359 through 370 Processing helix chain 'F' and resid 376 through 384 Processing helix chain 'F' and resid 386 through 396 removed outlier: 6.796A pdb=" N THR F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 408 removed outlier: 3.875A pdb=" N SER F 407 " --> pdb=" O SER F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 422 removed outlier: 3.707A pdb=" N THR F 421 " --> pdb=" O SER F 417 " (cutoff:3.500A) removed outlier: 4.338A 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 467 Processing helix chain 'F' and resid 489 through 500 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 605 through 608 removed outlier: 3.747A pdb=" N ASP F 608 " --> pdb=" O SER F 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 628 through 631 Processing helix chain 'F' and resid 653 through 655 No H-bonds generated for 'chain 'F' and resid 653 through 655' Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.551A pdb=" N LYS F 681 " --> pdb=" O SER F 678 " (cutoff:3.500A) 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 732 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 808 through 814 Processing helix chain 'J' and resid 138 through 145 Processing helix chain 'J' and resid 194 through 210 Processing helix chain 'J' and resid 265 through 269 Processing helix chain 'J' and resid 276 through 291 Processing helix chain 'J' and resid 332 through 335 removed outlier: 4.388A pdb=" N GLN J 335 " --> pdb=" O GLN J 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 332 through 335' Processing helix chain 'J' and resid 337 through 348 Processing helix chain 'J' and resid 359 through 366 removed outlier: 3.585A pdb=" N LEU J 366 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 38 removed outlier: 3.814A pdb=" N ASN K 26 " --> pdb=" O TRP K 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER K 28 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 56 Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'K' and resid 102 through 116 removed outlier: 3.946A pdb=" N SER K 115 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN K 116 " --> pdb=" O ALA K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 181 Processing helix chain 'K' and resid 194 through 196 No H-bonds generated for 'chain 'K' and resid 194 through 196' Processing helix chain 'K' and resid 237 through 242 Processing helix chain 'K' and resid 247 through 263 removed outlier: 5.340A pdb=" N TYR K 252 " --> pdb=" O THR K 249 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR K 263 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 288 Processing helix chain 'K' and resid 308 through 322 Processing helix chain 'K' and resid 333 through 346 Processing helix chain 'L' and resid 7 through 48 removed outlier: 3.818A pdb=" N VAL L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 75 removed outlier: 3.850A pdb=" N GLU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'L' and resid 109 through 135 Proline residue: L 131 - end of helix Processing helix chain 'L' and resid 164 through 176 removed outlier: 3.962A pdb=" N ARG L 176 " --> pdb=" O GLU L 172 " (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 237 Processing helix chain 'L' and resid 246 through 256 removed outlier: 3.658A pdb=" N LEU L 250 " --> pdb=" O ILE L 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG L 251 " --> pdb=" O GLY L 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN L 255 " --> pdb=" O ARG L 251 " (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 345 through 355 Processing helix chain 'L' and resid 359 through 370 Processing helix chain 'L' and resid 376 through 384 Processing helix chain 'L' and resid 386 through 396 removed outlier: 6.796A pdb=" N THR L 394 " --> pdb=" O LEU L 390 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER L 395 " --> pdb=" O ARG L 391 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 408 removed outlier: 3.875A pdb=" N SER L 407 " --> pdb=" O SER L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 422 removed outlier: 3.707A pdb=" N THR L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 4.338A 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 467 Processing helix chain 'L' and resid 489 through 500 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 605 through 608 removed outlier: 3.746A pdb=" N ASP L 608 " --> pdb=" O SER L 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 605 through 608' Processing helix chain 'L' and resid 628 through 631 Processing helix chain 'L' and resid 653 through 655 No H-bonds generated for 'chain 'L' and resid 653 through 655' Processing helix chain 'L' and resid 678 through 682 removed outlier: 3.552A pdb=" N LYS L 681 " --> pdb=" O SER L 678 " (cutoff:3.500A) 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 732 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 808 through 814 Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 194 through 210 Processing helix chain 'M' and resid 265 through 269 Processing helix chain 'M' and resid 276 through 291 Processing helix chain 'M' and resid 337 through 348 Processing helix chain 'M' and resid 359 through 366 removed outlier: 3.621A pdb=" N LEU M 366 " --> pdb=" O VAL M 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 38 removed outlier: 3.813A pdb=" N ASN N 26 " --> pdb=" O TRP N 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER N 28 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU N 33 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA N 36 " --> pdb=" O ARG N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 56 Processing helix chain 'N' and resid 91 through 96 Processing helix chain 'N' and resid 102 through 116 removed outlier: 3.946A pdb=" N SER N 115 " --> pdb=" O SER N 111 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN N 116 " --> pdb=" O ALA N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 181 Processing helix chain 'N' and resid 194 through 196 No H-bonds generated for 'chain 'N' and resid 194 through 196' Processing helix chain 'N' and resid 237 through 242 Processing helix chain 'N' and resid 247 through 263 removed outlier: 5.340A pdb=" N TYR N 252 " --> pdb=" O THR N 249 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR N 263 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 288 Processing helix chain 'N' and resid 308 through 322 Processing helix chain 'N' and resid 333 through 346 Processing helix chain 'O' and resid 7 through 48 removed outlier: 3.818A pdb=" N VAL O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER O 25 " --> pdb=" O GLY O 21 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR O 27 " --> pdb=" O THR O 23 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG O 28 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS O 29 " --> pdb=" O SER O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 75 removed outlier: 3.849A pdb=" N GLU O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 79 No H-bonds generated for 'chain 'O' and resid 77 through 79' Processing helix chain 'O' and resid 109 through 135 Proline residue: O 131 - end of helix Processing helix chain 'O' and resid 164 through 176 removed outlier: 3.962A pdb=" N ARG O 176 " --> pdb=" O GLU O 172 " (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 237 Processing helix chain 'O' and resid 246 through 256 removed outlier: 3.658A pdb=" N LEU O 250 " --> pdb=" O ILE O 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG O 251 " --> pdb=" O GLY O 247 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN O 255 " --> pdb=" O ARG O 251 " (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 345 through 355 Processing helix chain 'O' and resid 359 through 370 Processing helix chain 'O' and resid 376 through 384 Processing helix chain 'O' and resid 386 through 396 removed outlier: 6.796A pdb=" N THR O 394 " --> pdb=" O LEU O 390 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER O 395 " --> pdb=" O ARG O 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 400 through 408 removed outlier: 3.875A pdb=" N SER O 407 " --> pdb=" O SER O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 422 removed outlier: 3.707A pdb=" N THR O 421 " --> pdb=" O SER O 417 " (cutoff:3.500A) removed outlier: 4.339A 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 467 Processing helix chain 'O' and resid 489 through 500 Processing helix chain 'O' and resid 549 through 556 removed outlier: 3.813A pdb=" N THR O 556 " --> pdb=" O ALA O 552 " (cutoff:3.500A) 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 605 through 608 removed outlier: 3.747A pdb=" N ASP O 608 " --> pdb=" O SER O 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 605 through 608' Processing helix chain 'O' and resid 628 through 631 Processing helix chain 'O' and resid 653 through 655 No H-bonds generated for 'chain 'O' and resid 653 through 655' Processing helix chain 'O' and resid 678 through 682 removed outlier: 3.551A pdb=" N LYS O 681 " --> pdb=" O SER O 678 " (cutoff:3.500A) 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 732 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 808 through 814 Processing sheet with id= A, first strand: chain 'H' and resid 123 through 127 removed outlier: 6.115A pdb=" N VAL H 136 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS H 126 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL H 134 " --> pdb=" O CYS H 126 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG H 76 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE H 65 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 183 through 188 removed outlier: 6.183A pdb=" N ARG G 214 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL G 265 " --> pdb=" O ARG G 214 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE G 216 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP G 267 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 218 " --> pdb=" O ASP G 267 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL G 269 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 514 through 517 removed outlier: 6.063A pdb=" N GLY G 534 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE G 517 " --> pdb=" O GLY G 534 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL G 536 " --> pdb=" O ILE G 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'G' and resid 563 through 565 removed outlier: 5.890A pdb=" N CYS G 590 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 614 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL G 638 " --> pdb=" O LEU G 615 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL G 662 " --> pdb=" O LEU G 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'G' and resid 688 through 691 removed outlier: 6.381A pdb=" N SER G 715 " --> pdb=" O LEU G 689 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU G 691 " --> pdb=" O SER G 715 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER G 717 " --> pdb=" O LEU G 691 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU G 743 " --> pdb=" O ILE G 716 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE G 718 " --> pdb=" O GLU G 743 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER G 745 " --> pdb=" O ILE G 718 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR G 768 " --> pdb=" O LEU G 744 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU G 746 " --> pdb=" O TYR G 768 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 770 " --> pdb=" O LEU G 746 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY G 795 " --> pdb=" O MET G 769 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE G 771 " --> pdb=" O GLY G 795 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET G 797 " --> pdb=" O ILE G 771 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR G 820 " --> pdb=" O LEU G 796 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU G 798 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR G 822 " --> pdb=" O LEU G 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'G' and resid 472 through 475 removed outlier: 7.205A pdb=" N THR G 484 " --> pdb=" O VAL G 474 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 123 through 127 removed outlier: 6.115A pdb=" N VAL B 136 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS B 126 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 134 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ARG B 76 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE B 65 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 183 through 188 removed outlier: 6.183A pdb=" N ARG C 214 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 265 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 216 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP C 267 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 218 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL C 269 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 514 through 517 removed outlier: 6.063A pdb=" N GLY C 534 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE C 517 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 536 " --> pdb=" O ILE C 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 563 through 565 removed outlier: 5.890A pdb=" N CYS C 590 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 614 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL C 638 " --> pdb=" O LEU C 615 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 662 " --> pdb=" O LEU C 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 688 through 691 removed outlier: 6.381A pdb=" N SER C 715 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU C 691 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER C 717 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU C 743 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE C 718 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER C 745 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR C 768 " --> pdb=" O LEU C 744 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU C 746 " --> pdb=" O TYR C 768 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER C 770 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY C 795 " --> pdb=" O MET C 769 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE C 771 " --> pdb=" O GLY C 795 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET C 797 " --> pdb=" O ILE C 771 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR C 820 " --> pdb=" O LEU C 796 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LEU C 798 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 822 " --> pdb=" O LEU C 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 472 through 475 removed outlier: 7.205A pdb=" N THR C 484 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 123 through 127 removed outlier: 6.115A pdb=" N VAL E 136 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS E 126 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL E 134 " --> pdb=" O CYS E 126 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ARG E 76 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE E 65 " --> pdb=" O ARG E 76 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 183 through 188 removed outlier: 6.183A pdb=" N ARG F 214 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL F 265 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE F 216 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP F 267 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 218 " --> pdb=" O ASP F 267 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL F 269 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 514 through 517 removed outlier: 6.064A pdb=" N GLY F 534 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE F 517 " --> pdb=" O GLY F 534 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 536 " --> pdb=" O ILE F 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 563 through 565 removed outlier: 5.891A pdb=" N CYS F 590 " --> pdb=" O LEU F 564 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE F 614 " --> pdb=" O LEU F 591 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL F 638 " --> pdb=" O LEU F 615 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL F 662 " --> pdb=" O LEU F 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 688 through 691 removed outlier: 6.381A pdb=" N SER F 715 " --> pdb=" O LEU F 689 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU F 691 " --> pdb=" O SER F 715 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER F 717 " --> pdb=" O LEU F 691 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU F 743 " --> pdb=" O ILE F 716 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE F 718 " --> pdb=" O GLU F 743 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER F 745 " --> pdb=" O ILE F 718 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR F 768 " --> pdb=" O LEU F 744 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU F 746 " --> pdb=" O TYR F 768 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER F 770 " --> pdb=" O LEU F 746 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 795 " --> pdb=" O MET F 769 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE F 771 " --> pdb=" O GLY F 795 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET F 797 " --> pdb=" O ILE F 771 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR F 820 " --> pdb=" O LEU F 796 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LEU F 798 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR F 822 " --> pdb=" O LEU F 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 472 through 475 removed outlier: 7.205A pdb=" N THR F 484 " --> pdb=" O VAL F 474 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 123 through 127 removed outlier: 6.115A pdb=" N VAL K 136 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS K 126 " --> pdb=" O VAL K 134 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL K 134 " --> pdb=" O CYS K 126 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG K 76 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE K 65 " --> pdb=" O ARG K 76 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 183 through 188 removed outlier: 6.183A pdb=" N ARG L 214 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL L 265 " --> pdb=" O ARG L 214 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE L 216 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP L 267 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL L 218 " --> pdb=" O ASP L 267 " (cutoff:3.500A) removed outlier: 7.342A 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: 6.064A pdb=" N GLY L 534 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE L 517 " --> pdb=" O GLY L 534 " (cutoff:3.500A) removed outlier: 6.902A 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: 5.891A pdb=" N CYS L 590 " --> pdb=" O LEU L 564 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE L 614 " --> pdb=" O LEU L 591 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL L 638 " --> pdb=" O LEU L 615 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL L 662 " --> pdb=" O LEU L 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'L' and resid 688 through 691 removed outlier: 6.381A pdb=" N SER L 715 " --> pdb=" O LEU L 689 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU L 691 " --> pdb=" O SER L 715 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER L 717 " --> pdb=" O LEU L 691 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU L 743 " --> pdb=" O ILE L 716 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE L 718 " --> pdb=" O GLU L 743 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER L 745 " --> pdb=" O ILE L 718 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR L 768 " --> pdb=" O LEU L 744 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU L 746 " --> pdb=" O TYR L 768 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER L 770 " --> pdb=" O LEU L 746 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY L 795 " --> pdb=" O MET L 769 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE L 771 " --> pdb=" O GLY L 795 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET L 797 " --> pdb=" O ILE L 771 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR L 820 " --> pdb=" O LEU L 796 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU L 798 " --> pdb=" O THR L 820 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR L 822 " --> pdb=" O LEU L 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 472 through 475 removed outlier: 7.205A pdb=" N THR L 484 " --> pdb=" O VAL L 474 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 123 through 127 removed outlier: 6.115A pdb=" N VAL N 136 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N CYS N 126 " --> pdb=" O VAL N 134 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL N 134 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG N 76 " --> pdb=" O PHE N 65 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE N 65 " --> pdb=" O ARG N 76 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 183 through 188 removed outlier: 6.184A pdb=" N ARG O 214 " --> pdb=" O LEU O 263 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL O 265 " --> pdb=" O ARG O 214 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE O 216 " --> pdb=" O VAL O 265 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP O 267 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL O 218 " --> pdb=" O ASP O 267 " (cutoff:3.500A) removed outlier: 7.342A 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: 6.064A pdb=" N GLY O 534 " --> pdb=" O LEU O 515 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE O 517 " --> pdb=" O GLY O 534 " (cutoff:3.500A) removed outlier: 6.902A 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: 5.891A pdb=" N CYS O 590 " --> pdb=" O LEU O 564 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE O 614 " --> pdb=" O LEU O 591 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL O 638 " --> pdb=" O LEU O 615 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL O 662 " --> pdb=" O LEU O 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'O' and resid 688 through 691 removed outlier: 6.381A pdb=" N SER O 715 " --> pdb=" O LEU O 689 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU O 691 " --> pdb=" O SER O 715 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER O 717 " --> pdb=" O LEU O 691 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU O 743 " --> pdb=" O ILE O 716 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE O 718 " --> pdb=" O GLU O 743 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER O 745 " --> pdb=" O ILE O 718 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR O 768 " --> pdb=" O LEU O 744 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU O 746 " --> pdb=" O TYR O 768 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER O 770 " --> pdb=" O LEU O 746 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY O 795 " --> pdb=" O MET O 769 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE O 771 " --> pdb=" O GLY O 795 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET O 797 " --> pdb=" O ILE O 771 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR O 820 " --> pdb=" O LEU O 796 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU O 798 " --> pdb=" O THR O 820 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR O 822 " --> pdb=" O LEU O 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'O' and resid 472 through 475 removed outlier: 7.206A pdb=" N THR O 484 " --> pdb=" O VAL O 474 " (cutoff:3.500A) 1640 hydrogen bonds defined for protein. 4605 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: 14.53 Time building geometry restraints manager: 16.87 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: 8957 1.31 - 1.44: 13928 1.44 - 1.56: 31139 1.56 - 1.69: 49 1.69 - 1.82: 455 Bond restraints: 54528 Sorted by residual: bond pdb=" C1' BQO D 502 " pdb=" O4' BQO D 502 " ideal model delta sigma weight residual 1.279 1.470 -0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" C1' BQO M 502 " pdb=" O4' BQO M 502 " ideal model delta sigma weight residual 1.279 1.470 -0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" C1' BQO J 502 " pdb=" O4' BQO J 502 " ideal model delta sigma weight residual 1.279 1.470 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" C1' BQO A 502 " pdb=" O4' BQO A 502 " ideal model delta sigma weight residual 1.279 1.469 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C1' BQO I 502 " pdb=" O4' BQO I 502 " ideal model delta sigma weight residual 1.279 1.469 -0.190 2.00e-02 2.50e+03 8.99e+01 ... (remaining 54523 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.98: 1166 105.98 - 113.01: 29304 113.01 - 120.04: 20645 120.04 - 127.08: 21886 127.08 - 134.11: 694 Bond angle restraints: 73695 Sorted by residual: angle pdb=" PB DTP L 901 " pdb=" O3B DTP L 901 " pdb=" PG DTP L 901 " ideal model delta sigma weight residual 139.87 128.89 10.98 1.00e+00 1.00e+00 1.20e+02 angle pdb=" PB DTP F 901 " pdb=" O3B DTP F 901 " pdb=" PG DTP F 901 " ideal model delta sigma weight residual 139.87 128.92 10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" PA DTP L 901 " pdb=" O3A DTP L 901 " pdb=" PB DTP L 901 " ideal model delta sigma weight residual 136.83 126.02 10.81 1.00e+00 1.00e+00 1.17e+02 angle pdb=" PA DTP O 901 " pdb=" O3A DTP O 901 " pdb=" PB DTP O 901 " ideal model delta sigma weight residual 136.83 126.13 10.70 1.00e+00 1.00e+00 1.15e+02 angle pdb=" PA DTP C 901 " pdb=" O3A DTP C 901 " pdb=" PB DTP C 901 " ideal model delta sigma weight residual 136.83 126.15 10.68 1.00e+00 1.00e+00 1.14e+02 ... (remaining 73690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 32026 23.46 - 46.91: 1039 46.91 - 70.37: 143 70.37 - 93.82: 48 93.82 - 117.28: 5 Dihedral angle restraints: 33261 sinusoidal: 13971 harmonic: 19290 Sorted by residual: 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 -111.30 -68.70 0 5.00e+00 4.00e-02 1.89e+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 -111.31 -68.69 0 5.00e+00 4.00e-02 1.89e+02 dihedral pdb=" CA ASN L 506 " pdb=" C ASN L 506 " pdb=" N PRO L 507 " pdb=" CA PRO L 507 " ideal model delta harmonic sigma weight residual 180.00 -111.35 -68.65 0 5.00e+00 4.00e-02 1.89e+02 ... (remaining 33258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 6613 0.081 - 0.161: 1472 0.161 - 0.242: 150 0.242 - 0.322: 35 0.322 - 0.403: 5 Chirality restraints: 8275 Sorted by residual: chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CB ILE H 43 " pdb=" CA ILE H 43 " pdb=" CG1 ILE H 43 " pdb=" CG2 ILE H 43 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB ILE N 43 " pdb=" CA ILE N 43 " pdb=" CG1 ILE N 43 " pdb=" CG2 ILE N 43 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 8272 not shown) Planarity restraints: 9310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BQO A 502 " -0.632 2.00e-02 2.50e+03 4.86e-01 5.31e+03 pdb=" C1' BQO A 502 " 0.399 2.00e-02 2.50e+03 pdb=" C2' BQO A 502 " -0.489 2.00e-02 2.50e+03 pdb=" C3 BQO A 502 " 0.318 2.00e-02 2.50e+03 pdb=" C3' BQO A 502 " -0.413 2.00e-02 2.50e+03 pdb=" N1 BQO A 502 " -0.388 2.00e-02 2.50e+03 pdb=" O1 BQO A 502 " -0.042 2.00e-02 2.50e+03 pdb=" O3' BQO A 502 " 0.373 2.00e-02 2.50e+03 pdb=" O4' BQO A 502 " 0.874 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BQO M 502 " -0.622 2.00e-02 2.50e+03 4.85e-01 5.30e+03 pdb=" C1' BQO M 502 " 0.395 2.00e-02 2.50e+03 pdb=" C2' BQO M 502 " -0.475 2.00e-02 2.50e+03 pdb=" C3 BQO M 502 " 0.330 2.00e-02 2.50e+03 pdb=" C3' BQO M 502 " -0.417 2.00e-02 2.50e+03 pdb=" N1 BQO M 502 " -0.418 2.00e-02 2.50e+03 pdb=" O1 BQO M 502 " -0.009 2.00e-02 2.50e+03 pdb=" O3' BQO M 502 " 0.331 2.00e-02 2.50e+03 pdb=" O4' BQO M 502 " 0.886 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BQO J 502 " -0.613 2.00e-02 2.50e+03 4.82e-01 5.22e+03 pdb=" C1' BQO J 502 " 0.395 2.00e-02 2.50e+03 pdb=" C2' BQO J 502 " -0.482 2.00e-02 2.50e+03 pdb=" C3 BQO J 502 " 0.327 2.00e-02 2.50e+03 pdb=" C3' BQO J 502 " -0.420 2.00e-02 2.50e+03 pdb=" N1 BQO J 502 " -0.409 2.00e-02 2.50e+03 pdb=" O1 BQO J 502 " -0.009 2.00e-02 2.50e+03 pdb=" O3' BQO J 502 " 0.340 2.00e-02 2.50e+03 pdb=" O4' BQO J 502 " 0.870 2.00e-02 2.50e+03 ... (remaining 9307 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 10189 2.77 - 3.30: 51984 3.30 - 3.83: 88469 3.83 - 4.37: 106005 4.37 - 4.90: 172623 Nonbonded interactions: 429270 Sorted by model distance: nonbonded pdb=" OD1 ASP O 475 " pdb=" OG1 THR O 484 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP L 475 " pdb=" OG1 THR L 484 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP C 475 " pdb=" OG1 THR C 484 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP F 475 " pdb=" OG1 THR F 484 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASP G 475 " pdb=" OG1 THR G 484 " model vdw 2.234 2.440 ... (remaining 429265 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 'A' and (resid 135 through 367 or resid 501 or (resid 502 and (name N or \ name CA or name C or name O or name CB or name CG2 or name C1 or name C1' or nam \ e C2 or name C2' or name C3 or name C3' or name C4 or name C5 or name C6 or name \ N1 or name N3 or name O1 or name O2 or name O3' or name O4 or name O4' or name \ O5' or name OP1 or name P )))) selection = (chain 'D' and (resid 135 through 367 or resid 501 or (resid 502 and (name N or \ name CA or name C or name O or name CB or name CG2 or name C1 or name C1' or nam \ e C2 or name C2' or name C3 or name C3' or name C4 or name C5 or name C6 or name \ N1 or name N3 or name O1 or name O2 or name O3' or name O4 or name O4' or name \ O5' or name OP1 or name P )))) selection = chain 'I' selection = (chain 'J' and (resid 135 through 367 or resid 501 or (resid 502 and (name N or \ name CA or name C or name O or name CB or name CG2 or name C1 or name C1' or nam \ e C2 or name C2' or name C3 or name C3' or name C4 or name C5 or name C6 or name \ N1 or name N3 or name O1 or name O2 or name O3' or name O4 or name O4' or name \ O5' or name OP1 or name P )))) selection = (chain 'M' and (resid 135 through 367 or resid 501 or (resid 502 and (name N or \ name CA or name C or name O or name CB or name CG2 or name C1 or name C1' or nam \ e C2 or name C2' or name C3 or name C3' or name C4 or name C5 or name C6 or name \ N1 or name N3 or name O1 or name O2 or name O3' or name O4 or name O4' or name \ O5' or name OP1 or name P )))) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.710 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 102.380 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.380 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 : 0.010 0.191 54528 Z= 0.682 Angle : 1.224 14.104 73695 Z= 0.658 Chirality : 0.066 0.403 8275 Planarity : 0.014 0.486 9300 Dihedral : 12.695 117.276 20741 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.34 % Favored : 88.35 % Rotamer: Outliers : 0.59 % Allowed : 4.72 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.52 % Twisted General : 0.55 % 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: -4.25 (0.08), residues: 6550 helix: -2.45 (0.08), residues: 2620 sheet: -2.86 (0.17), residues: 615 loop : -3.16 (0.09), residues: 3315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP F 379 HIS 0.016 0.004 HIS F 438 PHE 0.041 0.004 PHE A 207 TYR 0.033 0.003 TYR F 768 ARG 0.014 0.002 ARG L 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1784 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1749 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 250 THR cc_start: 0.6696 (p) cc_final: 0.6482 (p) REVERT: I 361 GLU cc_start: 0.9538 (mp0) cc_final: 0.8858 (pp20) REVERT: H 171 GLU cc_start: 0.6663 (pt0) cc_final: 0.5978 (pt0) REVERT: H 174 ASN cc_start: 0.8560 (m-40) cc_final: 0.8217 (m110) REVERT: G 129 VAL cc_start: 0.8396 (t) cc_final: 0.8123 (m) REVERT: G 370 LEU cc_start: 0.8377 (tt) cc_final: 0.8066 (mt) REVERT: G 487 ILE cc_start: 0.5184 (pt) cc_final: 0.4874 (pt) REVERT: G 723 SER cc_start: 0.5619 (p) cc_final: 0.4746 (t) REVERT: B 171 GLU cc_start: 0.6544 (pt0) cc_final: 0.5851 (pt0) REVERT: B 174 ASN cc_start: 0.8276 (m-40) cc_final: 0.7856 (m110) REVERT: C 41 MET cc_start: 0.6689 (ttm) cc_final: 0.6379 (ttp) REVERT: C 370 LEU cc_start: 0.8461 (tt) cc_final: 0.8215 (mt) REVERT: C 487 ILE cc_start: 0.5463 (pt) cc_final: 0.5078 (pt) REVERT: C 521 PHE cc_start: 0.5323 (m-80) cc_final: 0.4878 (m-80) REVERT: C 723 SER cc_start: 0.5872 (p) cc_final: 0.5446 (t) REVERT: D 177 LEU cc_start: 0.8557 (mt) cc_final: 0.8313 (mm) REVERT: D 250 THR cc_start: 0.6944 (p) cc_final: 0.6724 (p) REVERT: E 171 GLU cc_start: 0.6780 (pt0) cc_final: 0.6003 (pt0) REVERT: E 174 ASN cc_start: 0.8609 (m-40) cc_final: 0.8157 (m110) REVERT: E 310 LEU cc_start: 0.9105 (tm) cc_final: 0.8726 (tp) REVERT: F 129 VAL cc_start: 0.8271 (t) cc_final: 0.7912 (m) REVERT: F 370 LEU cc_start: 0.8481 (tt) cc_final: 0.8212 (mt) REVERT: F 433 LYS cc_start: 0.7509 (tttt) cc_final: 0.7171 (ttpp) REVERT: F 723 SER cc_start: 0.5583 (p) cc_final: 0.5026 (t) REVERT: F 804 LEU cc_start: 0.7146 (tp) cc_final: 0.6068 (tp) REVERT: J 177 LEU cc_start: 0.8754 (mt) cc_final: 0.8224 (mp) REVERT: K 174 ASN cc_start: 0.8580 (m-40) cc_final: 0.8238 (m110) REVERT: L 23 THR cc_start: 0.8453 (p) cc_final: 0.8242 (p) REVERT: L 129 VAL cc_start: 0.8450 (t) cc_final: 0.8117 (m) REVERT: L 370 LEU cc_start: 0.8552 (tt) cc_final: 0.8174 (mt) REVERT: L 487 ILE cc_start: 0.5628 (pt) cc_final: 0.5310 (pt) REVERT: L 520 ASN cc_start: 0.6100 (t0) cc_final: 0.5898 (t0) REVERT: L 723 SER cc_start: 0.5198 (p) cc_final: 0.4700 (t) REVERT: N 171 GLU cc_start: 0.6455 (pt0) cc_final: 0.5732 (pt0) REVERT: N 174 ASN cc_start: 0.8444 (m-40) cc_final: 0.7971 (m110) REVERT: N 197 VAL cc_start: 0.8171 (t) cc_final: 0.7828 (t) REVERT: O 129 VAL cc_start: 0.8389 (t) cc_final: 0.7944 (m) REVERT: O 433 LYS cc_start: 0.7559 (tttt) cc_final: 0.7335 (tmtt) REVERT: O 723 SER cc_start: 0.5656 (p) cc_final: 0.5013 (t) outliers start: 35 outliers final: 8 residues processed: 1779 average time/residue: 0.5651 time to fit residues: 1651.5149 Evaluate side-chains 1003 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 995 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 313 GLU Chi-restraints excluded: chain N residue 121 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 553 optimal weight: 0.9990 chunk 496 optimal weight: 5.9990 chunk 275 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 334 optimal weight: 2.9990 chunk 265 optimal weight: 30.0000 chunk 513 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 382 optimal weight: 1.9990 chunk 594 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 179 ASN I 209 HIS H 59 ASN H 180 HIS H 189 HIS G 128 GLN G 288 GLN ** G 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 627 GLN G 643 ASN G 673 ASN G 698 GLN G 742 HIS G 747 GLN G 780 GLN ** G 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 151 ASN A 179 ASN A 209 HIS A 251 HIS B 59 ASN B 180 HIS B 189 HIS C 288 GLN C 385 HIS ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 HIS C 747 GLN C 780 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN D 179 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 180 HIS E 189 HIS F 288 GLN F 385 HIS ** F 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS F 627 GLN F 643 ASN F 673 ASN F 698 GLN F 742 HIS F 747 GLN F 780 GLN ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 142 ASN J 151 ASN J 179 ASN J 209 HIS J 251 HIS K 59 ASN K 180 HIS K 189 HIS ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN L 385 HIS L 438 HIS L 627 GLN L 643 ASN L 673 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 742 HIS L 747 GLN ** L 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 ASN M 179 ASN N 59 ASN N 180 HIS N 189 HIS O 288 GLN O 385 HIS O 438 HIS ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 643 ASN O 673 ASN O 698 GLN O 742 HIS O 747 GLN O 780 GLN ** O 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 54528 Z= 0.223 Angle : 0.884 20.803 73695 Z= 0.421 Chirality : 0.048 0.266 8275 Planarity : 0.006 0.093 9300 Dihedral : 11.180 112.342 7580 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.39 % Favored : 90.31 % Rotamer: Outliers : 3.42 % Allowed : 15.01 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.39 % 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: -3.07 (0.09), residues: 6550 helix: -1.03 (0.09), residues: 2700 sheet: -2.52 (0.18), residues: 660 loop : -2.87 (0.10), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 844 HIS 0.010 0.001 HIS I 209 PHE 0.025 0.002 PHE F 748 TYR 0.017 0.002 TYR M 143 ARG 0.011 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1066 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 177 LEU cc_start: 0.8632 (mm) cc_final: 0.8414 (mp) REVERT: I 195 MET cc_start: 0.1495 (ptt) cc_final: 0.1136 (ptm) REVERT: I 209 HIS cc_start: 0.7062 (m90) cc_final: 0.6741 (m90) REVERT: I 287 LEU cc_start: 0.8718 (mt) cc_final: 0.8421 (tt) REVERT: I 361 GLU cc_start: 0.9516 (mp0) cc_final: 0.8918 (pp20) REVERT: H 197 VAL cc_start: 0.8042 (t) cc_final: 0.7622 (m) REVERT: H 202 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.6944 (p0) REVERT: G 801 LEU cc_start: 0.6112 (tp) cc_final: 0.5685 (tp) REVERT: A 195 MET cc_start: 0.1507 (ptt) cc_final: 0.0898 (ptt) REVERT: B 85 MET cc_start: 0.7757 (mtt) cc_final: 0.7541 (mtt) REVERT: B 197 VAL cc_start: 0.8025 (t) cc_final: 0.7692 (m) REVERT: B 202 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7622 (p0) REVERT: B 258 LEU cc_start: 0.8801 (tp) cc_final: 0.8586 (tp) REVERT: C 801 LEU cc_start: 0.6303 (tp) cc_final: 0.5913 (tp) REVERT: D 195 MET cc_start: 0.1434 (ptt) cc_final: 0.1155 (ptt) REVERT: F 370 LEU cc_start: 0.8647 (tt) cc_final: 0.8318 (mt) REVERT: F 739 HIS cc_start: 0.6715 (p-80) cc_final: 0.6428 (p-80) REVERT: J 195 MET cc_start: 0.1310 (OUTLIER) cc_final: 0.0946 (ptt) REVERT: L 68 LEU cc_start: 0.8049 (mt) cc_final: 0.7812 (mt) REVERT: L 487 ILE cc_start: 0.6214 (pt) cc_final: 0.5534 (pt) REVERT: L 801 LEU cc_start: 0.6342 (tp) cc_final: 0.5966 (tp) REVERT: M 172 MET cc_start: 0.4331 (tpp) cc_final: 0.3928 (tpp) REVERT: M 195 MET cc_start: 0.1042 (ptt) cc_final: 0.0593 (ptm) REVERT: M 287 LEU cc_start: 0.8744 (mt) cc_final: 0.8326 (tt) REVERT: N 197 VAL cc_start: 0.8044 (t) cc_final: 0.7641 (m) REVERT: N 310 LEU cc_start: 0.9061 (mm) cc_final: 0.8772 (pp) REVERT: O 520 ASN cc_start: 0.6503 (t0) cc_final: 0.6278 (t0) REVERT: O 801 LEU cc_start: 0.5885 (tp) cc_final: 0.5548 (tp) outliers start: 203 outliers final: 72 residues processed: 1207 average time/residue: 0.5284 time to fit residues: 1076.5719 Evaluate side-chains 947 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 872 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 234 TYR Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 485 CYS Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 587 HIS Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain E residue 234 TYR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 560 TYR Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 718 ILE Chi-restraints excluded: chain F residue 771 ILE Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 282 PHE Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 172 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain L residue 360 LEU Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 384 GLU Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 639 LEU Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 330 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 495 optimal weight: 4.9990 chunk 405 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 595 optimal weight: 9.9990 chunk 643 optimal weight: 7.9990 chunk 530 optimal weight: 6.9990 chunk 590 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 478 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS H 154 ASN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 HIS G 236 ASN G 255 GLN G 385 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 780 GLN G 812 GLN B 154 ASN B 180 HIS C 210 HIS C 255 GLN C 438 HIS C 467 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 GLN C 812 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 154 ASN E 180 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 210 HIS ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN F 255 GLN F 438 HIS F 780 GLN F 812 GLN J 142 ASN J 209 HIS ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 HIS L 236 ASN L 255 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 812 GLN ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 HIS N 106 ASN N 180 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN O 210 HIS ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 255 GLN ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 780 GLN O 812 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.8194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 54528 Z= 0.494 Angle : 1.045 20.230 73695 Z= 0.519 Chirality : 0.054 0.243 8275 Planarity : 0.008 0.111 9300 Dihedral : 10.662 98.975 7561 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.82 % Favored : 87.88 % Rotamer: Outliers : 5.37 % Allowed : 15.60 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.47 % 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: -2.78 (0.10), residues: 6550 helix: -0.73 (0.09), residues: 2710 sheet: -2.48 (0.18), residues: 615 loop : -2.76 (0.10), residues: 3225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP H 74 HIS 0.082 0.003 HIS A 251 PHE 0.039 0.004 PHE E 30 TYR 0.029 0.003 TYR O 109 ARG 0.017 0.001 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 802 time to evaluate : 4.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 138 LEU cc_start: 0.8554 (mt) cc_final: 0.8243 (pt) REVERT: I 177 LEU cc_start: 0.8936 (mm) cc_final: 0.8677 (mp) REVERT: I 195 MET cc_start: 0.2877 (ptt) cc_final: 0.2574 (ptm) REVERT: I 216 ILE cc_start: 0.5381 (mm) cc_final: 0.4972 (mt) REVERT: I 217 TYR cc_start: 0.4431 (OUTLIER) cc_final: 0.2486 (m-80) REVERT: I 220 PHE cc_start: 0.5176 (OUTLIER) cc_final: 0.4687 (t80) REVERT: I 287 LEU cc_start: 0.8901 (mt) cc_final: 0.8618 (tt) REVERT: I 361 GLU cc_start: 0.9575 (mp0) cc_final: 0.8967 (pp20) REVERT: H 85 MET cc_start: 0.7333 (mtt) cc_final: 0.6796 (mtt) REVERT: H 124 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8784 (mp) REVERT: H 177 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8080 (p) REVERT: G 28 ARG cc_start: 0.6709 (mpp-170) cc_final: 0.6139 (mpp-170) REVERT: G 203 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7500 (p90) REVERT: G 431 ILE cc_start: 0.8704 (mp) cc_final: 0.8499 (mm) REVERT: G 623 LEU cc_start: 0.8138 (mt) cc_final: 0.7847 (mp) REVERT: G 728 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8084 (tt) REVERT: G 769 MET cc_start: 0.7344 (tmm) cc_final: 0.6371 (tmm) REVERT: A 172 MET cc_start: 0.3374 (tpp) cc_final: 0.2844 (tpp) REVERT: A 195 MET cc_start: 0.2848 (ptt) cc_final: 0.2457 (ptm) REVERT: B 151 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8096 (m) REVERT: B 202 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8277 (p0) REVERT: B 276 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7916 (pp) REVERT: C 203 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7509 (p90) REVERT: C 226 GLU cc_start: 0.8592 (mp0) cc_final: 0.8289 (mp0) REVERT: C 278 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7755 (p0) REVERT: C 431 ILE cc_start: 0.8771 (mp) cc_final: 0.8437 (mm) REVERT: D 276 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6291 (tptt) REVERT: E 191 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6963 (p0) REVERT: E 192 VAL cc_start: 0.9305 (t) cc_final: 0.9102 (p) REVERT: E 276 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7896 (pp) REVERT: E 310 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8716 (tm) REVERT: F 203 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7668 (p90) REVERT: F 278 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7215 (p0) REVERT: F 622 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8490 (p0) REVERT: F 788 ASN cc_start: 0.7341 (p0) cc_final: 0.7047 (p0) REVERT: J 172 MET cc_start: 0.3663 (tpp) cc_final: 0.3322 (tpt) REVERT: K 163 SER cc_start: 0.8801 (p) cc_final: 0.8573 (m) REVERT: K 210 LEU cc_start: 0.9303 (pp) cc_final: 0.9050 (pp) REVERT: L 203 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6712 (p90) REVERT: L 278 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7498 (p0) REVERT: L 431 ILE cc_start: 0.8627 (mp) cc_final: 0.8354 (mm) REVERT: M 167 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6548 (mm) REVERT: M 172 MET cc_start: 0.4447 (tpp) cc_final: 0.4186 (tpp) REVERT: M 195 MET cc_start: 0.2501 (OUTLIER) cc_final: 0.1522 (ptm) REVERT: N 191 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7015 (p0) REVERT: N 276 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7495 (pp) REVERT: O 29 LYS cc_start: 0.8372 (ptpp) cc_final: 0.8097 (ptpp) REVERT: O 70 TYR cc_start: 0.7855 (m-10) cc_final: 0.7500 (m-10) REVERT: O 203 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7658 (p90) REVERT: O 623 LEU cc_start: 0.8185 (mt) cc_final: 0.7904 (mp) outliers start: 319 outliers final: 135 residues processed: 1060 average time/residue: 0.5010 time to fit residues: 898.4160 Evaluate side-chains 777 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 617 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 220 PHE Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 302 LYS Chi-restraints excluded: chain H residue 315 CYS Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 373 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 563 VAL Chi-restraints excluded: chain G residue 587 HIS Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 728 LEU Chi-restraints excluded: chain G residue 736 THR Chi-restraints excluded: chain G residue 746 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain G residue 771 ILE Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 622 ASN Chi-restraints excluded: chain F residue 658 VAL Chi-restraints excluded: chain F residue 718 ILE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain J residue 322 PHE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 266 MET Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 360 LEU Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 714 MET Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 723 SER Chi-restraints excluded: chain L residue 728 LEU Chi-restraints excluded: chain L residue 736 THR Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 771 ILE Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 322 PHE Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 315 CYS Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 437 VAL Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 658 VAL Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 736 THR Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 588 optimal weight: 0.7980 chunk 448 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 598 optimal weight: 0.9980 chunk 633 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 566 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN H 342 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 GLN A 146 GLN B 154 ASN C 525 GLN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 672 ASN ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN L 128 GLN L 322 ASN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 685 ASN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 322 ASN ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.8613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 54528 Z= 0.213 Angle : 0.845 17.327 73695 Z= 0.399 Chirality : 0.048 0.271 8275 Planarity : 0.005 0.087 9300 Dihedral : 10.043 92.997 7561 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.63 % Favored : 91.04 % Rotamer: Outliers : 3.86 % Allowed : 18.26 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.38 % 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: -2.26 (0.10), residues: 6550 helix: -0.16 (0.10), residues: 2725 sheet: -2.24 (0.19), residues: 625 loop : -2.60 (0.10), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 74 HIS 0.007 0.001 HIS G 587 PHE 0.024 0.002 PHE B 244 TYR 0.030 0.002 TYR L 109 ARG 0.010 0.001 ARG J 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 757 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 195 MET cc_start: 0.2296 (OUTLIER) cc_final: 0.1763 (ptm) REVERT: I 209 HIS cc_start: 0.7241 (m90) cc_final: 0.6918 (m90) REVERT: I 217 TYR cc_start: 0.4078 (OUTLIER) cc_final: 0.2408 (m-80) REVERT: I 287 LEU cc_start: 0.8775 (mt) cc_final: 0.8516 (tt) REVERT: I 361 GLU cc_start: 0.9555 (mp0) cc_final: 0.8881 (pp20) REVERT: H 202 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7737 (p0) REVERT: G 203 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7190 (p90) REVERT: G 769 MET cc_start: 0.7146 (tmm) cc_final: 0.6652 (tmm) REVERT: A 172 MET cc_start: 0.3058 (tpp) cc_final: 0.2577 (tpp) REVERT: A 205 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 210 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8006 (mp0) REVERT: A 361 GLU cc_start: 0.9516 (mp0) cc_final: 0.8916 (pp20) REVERT: B 202 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8057 (p0) REVERT: C 203 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6917 (p90) REVERT: C 303 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8386 (ptpp) REVERT: D 195 MET cc_start: 0.2660 (ptt) cc_final: 0.2436 (ptm) REVERT: D 205 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8253 (mt) REVERT: D 219 ASP cc_start: 0.5912 (p0) cc_final: 0.5570 (p0) REVERT: E 145 MET cc_start: 0.8117 (ptp) cc_final: 0.7915 (mpp) REVERT: E 310 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (tm) REVERT: F 203 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7312 (p90) REVERT: F 278 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7378 (p0) REVERT: F 788 ASN cc_start: 0.7455 (p0) cc_final: 0.7109 (p0) REVERT: F 797 MET cc_start: 0.7154 (ppp) cc_final: 0.6792 (ppp) REVERT: J 172 MET cc_start: 0.3330 (tpp) cc_final: 0.2836 (tpp) REVERT: K 122 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (mm-40) REVERT: K 210 LEU cc_start: 0.9321 (pp) cc_final: 0.9069 (pp) REVERT: L 116 GLN cc_start: 0.8073 (mt0) cc_final: 0.7845 (mt0) REVERT: L 203 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7111 (p90) REVERT: L 278 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7386 (p0) REVERT: M 172 MET cc_start: 0.4195 (tpp) cc_final: 0.3794 (tpp) REVERT: M 195 MET cc_start: 0.2285 (OUTLIER) cc_final: 0.1308 (ptm) REVERT: N 85 MET cc_start: 0.7855 (mtt) cc_final: 0.7199 (mmt) REVERT: N 276 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7867 (pp) REVERT: O 71 GLU cc_start: 0.7609 (tp30) cc_final: 0.7325 (tp30) REVERT: O 75 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8413 (mt) REVERT: O 203 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7250 (p90) REVERT: O 623 LEU cc_start: 0.8041 (mt) cc_final: 0.7783 (mt) outliers start: 229 outliers final: 107 residues processed: 935 average time/residue: 0.4956 time to fit residues: 785.5392 Evaluate side-chains 768 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 642 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 195 MET Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 244 PHE Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 373 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 563 VAL Chi-restraints excluded: chain G residue 587 HIS Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 686 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 718 ILE Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 287 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 723 SER Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 266 MET Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 360 LEU Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 709 ASN Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 723 SER Chi-restraints excluded: chain L residue 728 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 807 ASP Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 322 PHE Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 422 LEU Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 526 ILE Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 658 VAL Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 527 optimal weight: 0.0270 chunk 359 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 471 optimal weight: 0.9980 chunk 261 optimal weight: 0.4980 chunk 540 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 0.0980 chunk 568 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN H 154 ASN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN F 525 GLN F 672 ASN ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN L 128 GLN L 434 GLN ** L 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN O 434 GLN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.9159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54528 Z= 0.228 Angle : 0.820 17.277 73695 Z= 0.386 Chirality : 0.047 0.262 8275 Planarity : 0.005 0.100 9300 Dihedral : 9.460 87.147 7561 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.32 % Favored : 89.45 % Rotamer: Outliers : 3.89 % Allowed : 18.97 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.22 % 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: -1.96 (0.10), residues: 6550 helix: 0.11 (0.10), residues: 2720 sheet: -2.03 (0.20), residues: 585 loop : -2.48 (0.10), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP L 844 HIS 0.007 0.001 HIS J 180 PHE 0.023 0.002 PHE N 30 TYR 0.015 0.001 TYR F 425 ARG 0.006 0.000 ARG H 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 687 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 178 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7614 (mm-30) REVERT: I 209 HIS cc_start: 0.7573 (m90) cc_final: 0.7332 (m90) REVERT: I 217 TYR cc_start: 0.3664 (OUTLIER) cc_final: 0.2438 (m-80) REVERT: I 287 LEU cc_start: 0.8801 (mt) cc_final: 0.8535 (tt) REVERT: I 361 GLU cc_start: 0.9485 (mp0) cc_final: 0.8824 (tm-30) REVERT: H 177 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8230 (p) REVERT: H 202 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7975 (p0) REVERT: H 276 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7569 (pp) REVERT: G 37 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7320 (mm-30) REVERT: G 128 GLN cc_start: 0.7899 (mt0) cc_final: 0.7318 (mt0) REVERT: G 203 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7133 (p90) REVERT: A 172 MET cc_start: 0.3218 (tpp) cc_final: 0.2846 (tpp) REVERT: A 195 MET cc_start: 0.3204 (ptt) cc_final: 0.2831 (ptm) REVERT: A 205 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 209 HIS cc_start: 0.7725 (m90) cc_final: 0.7363 (m-70) REVERT: A 210 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8052 (mp0) REVERT: A 361 GLU cc_start: 0.9505 (mp0) cc_final: 0.8894 (pp20) REVERT: B 202 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8289 (p0) REVERT: B 269 MET cc_start: 0.5130 (mtm) cc_final: 0.4888 (mtm) REVERT: C 203 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6818 (p90) REVERT: C 226 GLU cc_start: 0.8374 (mp0) cc_final: 0.8172 (mp0) REVERT: C 303 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8433 (ptpp) REVERT: C 797 MET cc_start: 0.7781 (ppp) cc_final: 0.7262 (ppp) REVERT: D 219 ASP cc_start: 0.5997 (p0) cc_final: 0.5675 (p0) REVERT: E 145 MET cc_start: 0.8057 (ptp) cc_final: 0.7848 (mpp) REVERT: E 192 VAL cc_start: 0.9358 (t) cc_final: 0.9124 (p) REVERT: E 333 MET cc_start: 0.7776 (pmm) cc_final: 0.7530 (pmm) REVERT: F 203 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7258 (p90) REVERT: F 278 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7676 (p0) REVERT: F 728 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8072 (tt) REVERT: F 765 MET cc_start: 0.7928 (ppp) cc_final: 0.7307 (ppp) REVERT: F 788 ASN cc_start: 0.7422 (p0) cc_final: 0.7064 (p0) REVERT: F 797 MET cc_start: 0.7285 (ppp) cc_final: 0.7012 (ppp) REVERT: J 172 MET cc_start: 0.3498 (tpp) cc_final: 0.2699 (tpp) REVERT: J 205 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8386 (mt) REVERT: L 203 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7196 (p90) REVERT: L 278 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7437 (p0) REVERT: L 769 MET cc_start: 0.7046 (tmm) cc_final: 0.6784 (ttp) REVERT: M 172 MET cc_start: 0.4230 (tpp) cc_final: 0.3807 (tpp) REVERT: M 325 MET cc_start: 0.4849 (mmt) cc_final: 0.4533 (mmp) REVERT: M 361 GLU cc_start: 0.9473 (mp0) cc_final: 0.8717 (pp20) REVERT: N 85 MET cc_start: 0.7795 (mtt) cc_final: 0.7114 (mtt) REVERT: O 71 GLU cc_start: 0.7679 (tp30) cc_final: 0.7478 (tp30) REVERT: O 75 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (mt) REVERT: O 203 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7177 (p90) REVERT: O 428 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7000 (p0) outliers start: 231 outliers final: 134 residues processed: 861 average time/residue: 0.5013 time to fit residues: 727.7350 Evaluate side-chains 761 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 609 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain H residue 302 LYS Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 373 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 526 ILE Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 563 VAL Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 686 LEU Chi-restraints excluded: chain G residue 704 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 718 ILE Chi-restraints excluded: chain G residue 807 ASP Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 723 SER Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 266 MET Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 301 VAL Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 709 ASN Chi-restraints excluded: chain L residue 716 ILE Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 723 SER Chi-restraints excluded: chain L residue 728 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain M residue 322 PHE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 234 TYR Chi-restraints excluded: chain O residue 32 GLU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 428 ASP Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 704 LEU Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 213 optimal weight: 2.9990 chunk 570 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 633 optimal weight: 0.8980 chunk 526 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN G 414 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 ASN L 525 GLN ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 525 GLN ** O 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 1.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 54528 Z= 0.417 Angle : 0.930 20.989 73695 Z= 0.449 Chirality : 0.051 0.369 8275 Planarity : 0.006 0.080 9300 Dihedral : 9.636 88.707 7561 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.25 % Favored : 88.47 % Rotamer: Outliers : 4.55 % Allowed : 18.65 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.35 % 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: -2.10 (0.10), residues: 6550 helix: -0.04 (0.10), residues: 2735 sheet: -2.02 (0.20), residues: 570 loop : -2.55 (0.10), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP N 203 HIS 0.013 0.002 HIS E 142 PHE 0.027 0.002 PHE C 748 TYR 0.028 0.002 TYR C 425 ARG 0.006 0.001 ARG O 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 603 time to evaluate : 4.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 209 HIS cc_start: 0.7717 (m90) cc_final: 0.7451 (m90) REVERT: I 217 TYR cc_start: 0.3810 (OUTLIER) cc_final: 0.2270 (m-80) REVERT: I 287 LEU cc_start: 0.8960 (mt) cc_final: 0.8726 (tt) REVERT: I 361 GLU cc_start: 0.9530 (mp0) cc_final: 0.8886 (pp20) REVERT: H 202 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8423 (p0) REVERT: H 276 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7965 (pp) REVERT: H 301 MET cc_start: 0.7765 (mmm) cc_final: 0.7375 (mmm) REVERT: G 37 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7323 (mm-30) REVERT: G 120 GLU cc_start: 0.7741 (pp20) cc_final: 0.7520 (pp20) REVERT: G 128 GLN cc_start: 0.8028 (mt0) cc_final: 0.7577 (mt0) REVERT: G 203 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7069 (p90) REVERT: G 226 GLU cc_start: 0.8225 (mp0) cc_final: 0.7849 (mp0) REVERT: A 172 MET cc_start: 0.3594 (tpp) cc_final: 0.3053 (tpp) REVERT: A 195 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.4254 (ptm) REVERT: A 210 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8104 (mp0) REVERT: A 257 ILE cc_start: 0.7547 (mm) cc_final: 0.7114 (pt) REVERT: A 326 ASP cc_start: 0.5357 (t0) cc_final: 0.4583 (t0) REVERT: A 361 GLU cc_start: 0.9495 (mp0) cc_final: 0.8957 (pp20) REVERT: B 301 MET cc_start: 0.8052 (mmm) cc_final: 0.7593 (mmm) REVERT: C 203 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7090 (p90) REVERT: C 797 MET cc_start: 0.7744 (ppp) cc_final: 0.7505 (ppp) REVERT: D 195 MET cc_start: 0.4209 (ptt) cc_final: 0.3945 (ptm) REVERT: D 257 ILE cc_start: 0.7477 (mm) cc_final: 0.7006 (pt) REVERT: D 326 ASP cc_start: 0.4868 (t0) cc_final: 0.4202 (t0) REVERT: E 152 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8109 (tp) REVERT: E 301 MET cc_start: 0.7843 (mmm) cc_final: 0.7445 (mmm) REVERT: E 310 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8799 (tm) REVERT: F 203 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7582 (p90) REVERT: F 634 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7200 (mmmt) REVERT: F 765 MET cc_start: 0.8210 (ppp) cc_final: 0.7323 (ppp) REVERT: F 788 ASN cc_start: 0.7718 (p0) cc_final: 0.7186 (p0) REVERT: J 172 MET cc_start: 0.3998 (tpp) cc_final: 0.3654 (tpp) REVERT: J 257 ILE cc_start: 0.7424 (mm) cc_final: 0.7003 (pt) REVERT: J 326 ASP cc_start: 0.5304 (t0) cc_final: 0.4603 (t0) REVERT: K 191 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7295 (p0) REVERT: K 276 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7980 (pp) REVERT: K 301 MET cc_start: 0.8034 (mmm) cc_final: 0.7655 (mmm) REVERT: L 203 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.6823 (p90) REVERT: L 226 GLU cc_start: 0.8291 (mp0) cc_final: 0.7858 (mp0) REVERT: L 278 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7457 (p0) REVERT: M 172 MET cc_start: 0.4350 (tpp) cc_final: 0.3911 (tpp) REVERT: M 195 MET cc_start: 0.4972 (ptm) cc_final: 0.4655 (ptm) REVERT: M 257 ILE cc_start: 0.7435 (mm) cc_final: 0.7031 (pt) REVERT: M 325 MET cc_start: 0.4728 (mmm) cc_final: 0.4528 (mmp) REVERT: N 85 MET cc_start: 0.7923 (mtt) cc_final: 0.7698 (mmm) REVERT: N 141 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: N 301 MET cc_start: 0.8151 (mmm) cc_final: 0.7861 (mmm) REVERT: O 28 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7089 (tpp80) REVERT: O 71 GLU cc_start: 0.7788 (tp30) cc_final: 0.7570 (tp30) REVERT: O 203 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7539 (p90) REVERT: O 278 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7596 (p0) REVERT: O 659 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7904 (mtmm) outliers start: 270 outliers final: 165 residues processed: 810 average time/residue: 0.4925 time to fit residues: 674.2361 Evaluate side-chains 703 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 521 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain H residue 302 LYS Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 415 LEU Chi-restraints excluded: chain G residue 449 ARG Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 563 VAL Chi-restraints excluded: chain G residue 587 HIS Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 626 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 686 LEU Chi-restraints excluded: chain G residue 704 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 716 ILE Chi-restraints excluded: chain G residue 723 SER Chi-restraints excluded: chain G residue 736 THR Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 807 ASP Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 807 ASP Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 234 TYR Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 718 ILE Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain F residue 778 LYS Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain J residue 322 PHE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 132 PHE Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 266 MET Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 301 VAL Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 526 ILE Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 686 LEU Chi-restraints excluded: chain L residue 704 LEU Chi-restraints excluded: chain L residue 709 ASN Chi-restraints excluded: chain L residue 716 ILE Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 723 SER Chi-restraints excluded: chain L residue 736 THR Chi-restraints excluded: chain L residue 743 GLU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 234 TYR Chi-restraints excluded: chain N residue 262 ILE Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 278 ASP Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 460 ASP Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 526 ILE Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 657 LEU Chi-restraints excluded: chain O residue 659 LYS Chi-restraints excluded: chain O residue 686 LEU Chi-restraints excluded: chain O residue 704 LEU Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 736 THR Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 797 MET Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 611 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 361 optimal weight: 8.9990 chunk 462 optimal weight: 5.9990 chunk 358 optimal weight: 0.9980 chunk 533 optimal weight: 0.7980 chunk 353 optimal weight: 4.9990 chunk 631 optimal weight: 0.9990 chunk 395 optimal weight: 40.0000 chunk 384 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 ASN ** G 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 146 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS C 467 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 672 ASN ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 611 ASN ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN ** N 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 595 ASN O 611 ASN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 672 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 1.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54528 Z= 0.196 Angle : 0.830 17.173 73695 Z= 0.388 Chirality : 0.047 0.232 8275 Planarity : 0.005 0.112 9300 Dihedral : 9.136 89.779 7561 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.33 % Favored : 90.44 % Rotamer: Outliers : 2.88 % Allowed : 20.66 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.25 % 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: -1.83 (0.10), residues: 6550 helix: 0.21 (0.10), residues: 2710 sheet: -1.81 (0.20), residues: 560 loop : -2.41 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 203 HIS 0.008 0.001 HIS J 209 PHE 0.036 0.002 PHE K 244 TYR 0.013 0.001 TYR O 27 ARG 0.007 0.000 ARG J 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 641 time to evaluate : 4.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 217 TYR cc_start: 0.4034 (OUTLIER) cc_final: 0.3623 (m-80) REVERT: I 257 ILE cc_start: 0.7263 (mm) cc_final: 0.6731 (pt) REVERT: I 287 LEU cc_start: 0.8951 (mt) cc_final: 0.8706 (tt) REVERT: H 202 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8290 (p0) REVERT: H 301 MET cc_start: 0.7745 (mmm) cc_final: 0.7332 (mmm) REVERT: G 37 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7318 (mm-30) REVERT: G 203 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7096 (p90) REVERT: G 797 MET cc_start: 0.7488 (ppp) cc_final: 0.6775 (ppp) REVERT: A 172 MET cc_start: 0.3918 (tpp) cc_final: 0.3428 (tpp) REVERT: A 195 MET cc_start: 0.4484 (OUTLIER) cc_final: 0.4042 (ptm) REVERT: A 205 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 257 ILE cc_start: 0.7536 (mm) cc_final: 0.7166 (pt) REVERT: A 326 ASP cc_start: 0.5229 (t0) cc_final: 0.4527 (t0) REVERT: A 361 GLU cc_start: 0.9460 (mp0) cc_final: 0.8943 (pp20) REVERT: B 301 MET cc_start: 0.8246 (mmm) cc_final: 0.7745 (mmm) REVERT: C 203 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.6838 (p90) REVERT: C 405 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 195 MET cc_start: 0.3969 (ptt) cc_final: 0.3679 (ptm) REVERT: D 257 ILE cc_start: 0.7625 (mm) cc_final: 0.7252 (pt) REVERT: D 326 ASP cc_start: 0.4855 (t0) cc_final: 0.4238 (t0) REVERT: E 301 MET cc_start: 0.7912 (mmm) cc_final: 0.7574 (mmm) REVERT: E 310 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (tm) REVERT: F 203 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7386 (p90) REVERT: F 405 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7588 (tm-30) REVERT: F 449 ARG cc_start: 0.7542 (tpm170) cc_final: 0.7254 (tpm170) REVERT: F 765 MET cc_start: 0.7862 (ppp) cc_final: 0.7450 (ppp) REVERT: F 788 ASN cc_start: 0.7495 (p0) cc_final: 0.6977 (p0) REVERT: J 172 MET cc_start: 0.3921 (tpp) cc_final: 0.3584 (tpp) REVERT: J 195 MET cc_start: 0.4068 (ptm) cc_final: 0.3378 (ptm) REVERT: J 257 ILE cc_start: 0.7542 (mm) cc_final: 0.7194 (pt) REVERT: K 276 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8016 (pp) REVERT: K 301 MET cc_start: 0.8073 (mmm) cc_final: 0.7658 (mmm) REVERT: K 315 CYS cc_start: 0.8383 (t) cc_final: 0.8166 (m) REVERT: L 113 LYS cc_start: 0.8516 (mptt) cc_final: 0.8115 (ptpp) REVERT: L 203 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.6928 (p90) REVERT: L 278 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7321 (p0) REVERT: L 405 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7629 (tm-30) REVERT: M 172 MET cc_start: 0.4264 (tpp) cc_final: 0.3852 (tpp) REVERT: M 194 ARG cc_start: 0.7330 (mpt-90) cc_final: 0.6870 (mpt-90) REVERT: M 195 MET cc_start: 0.4567 (ptm) cc_final: 0.3754 (ptm) REVERT: M 257 ILE cc_start: 0.7405 (mm) cc_final: 0.7019 (pt) REVERT: M 361 GLU cc_start: 0.9485 (mp0) cc_final: 0.8755 (pp20) REVERT: O 203 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7227 (p90) REVERT: O 405 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7690 (tm-30) REVERT: O 565 ASP cc_start: 0.6418 (p0) cc_final: 0.6184 (p0) REVERT: O 769 MET cc_start: 0.6933 (tpp) cc_final: 0.6517 (tpp) outliers start: 171 outliers final: 112 residues processed: 765 average time/residue: 0.5002 time to fit residues: 646.0526 Evaluate side-chains 680 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 556 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 626 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 672 ASN Chi-restraints excluded: chain G residue 704 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 718 ILE Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 TYR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 301 VAL Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 704 LEU Chi-restraints excluded: chain L residue 716 ILE Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 244 PHE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 321 ASP Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 422 LEU Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 704 LEU Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 797 MET Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 390 optimal weight: 0.0980 chunk 252 optimal weight: 9.9990 chunk 377 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 401 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 58 optimal weight: 0.0970 chunk 496 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN G 128 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 ASN G 780 GLN ** G 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 332 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 511 ASN L 611 ASN ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 780 GLN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 672 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 1.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54528 Z= 0.183 Angle : 0.829 17.242 73695 Z= 0.384 Chirality : 0.047 0.221 8275 Planarity : 0.005 0.112 9300 Dihedral : 8.855 84.730 7561 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.66 % Favored : 90.15 % Rotamer: Outliers : 2.58 % Allowed : 21.43 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.24 % 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: -1.69 (0.10), residues: 6550 helix: 0.39 (0.10), residues: 2670 sheet: -1.80 (0.20), residues: 585 loop : -2.35 (0.11), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 203 HIS 0.013 0.001 HIS M 209 PHE 0.026 0.001 PHE L 386 TYR 0.011 0.001 TYR O 27 ARG 0.006 0.000 ARG J 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 624 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 172 MET cc_start: 0.3003 (tpp) cc_final: 0.1273 (tpp) REVERT: I 178 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7721 (mm-30) REVERT: I 257 ILE cc_start: 0.7302 (mm) cc_final: 0.6779 (pt) REVERT: I 287 LEU cc_start: 0.8927 (mt) cc_final: 0.8684 (tt) REVERT: I 361 GLU cc_start: 0.9435 (mp0) cc_final: 0.8654 (pp20) REVERT: H 202 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8253 (p0) REVERT: H 301 MET cc_start: 0.7925 (mmm) cc_final: 0.7673 (mmm) REVERT: G 37 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7504 (mm-30) REVERT: G 203 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7169 (p90) REVERT: A 172 MET cc_start: 0.3755 (tpp) cc_final: 0.3357 (tpp) REVERT: A 195 MET cc_start: 0.4355 (OUTLIER) cc_final: 0.3958 (ptm) REVERT: A 257 ILE cc_start: 0.7566 (mm) cc_final: 0.7221 (pt) REVERT: A 361 GLU cc_start: 0.9468 (mp0) cc_final: 0.8921 (pp20) REVERT: B 301 MET cc_start: 0.8166 (mmm) cc_final: 0.7628 (mmm) REVERT: C 203 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6631 (p90) REVERT: C 405 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7673 (tm-30) REVERT: D 172 MET cc_start: 0.3435 (tpp) cc_final: 0.3079 (tpp) REVERT: D 195 MET cc_start: 0.4133 (ptt) cc_final: 0.3760 (ptm) REVERT: D 257 ILE cc_start: 0.7641 (mm) cc_final: 0.7283 (pt) REVERT: D 326 ASP cc_start: 0.4986 (t0) cc_final: 0.4351 (t0) REVERT: E 145 MET cc_start: 0.7032 (ppp) cc_final: 0.6758 (ppp) REVERT: E 301 MET cc_start: 0.7946 (mmm) cc_final: 0.7609 (mmm) REVERT: E 310 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8575 (tm) REVERT: F 203 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7263 (p90) REVERT: F 405 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7560 (tm-30) REVERT: F 686 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8657 (pp) REVERT: F 765 MET cc_start: 0.7795 (ppp) cc_final: 0.7320 (ppp) REVERT: F 788 ASN cc_start: 0.7362 (p0) cc_final: 0.6776 (p0) REVERT: J 137 TRP cc_start: 0.7300 (t-100) cc_final: 0.6761 (t-100) REVERT: J 172 MET cc_start: 0.3662 (tpp) cc_final: 0.3211 (tpp) REVERT: J 195 MET cc_start: 0.4107 (ptm) cc_final: 0.3362 (ptm) REVERT: J 257 ILE cc_start: 0.7526 (mm) cc_final: 0.7215 (pt) REVERT: K 301 MET cc_start: 0.8058 (mmm) cc_final: 0.7621 (mmm) REVERT: L 203 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7062 (p90) REVERT: L 278 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7324 (p0) REVERT: L 405 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7491 (tm-30) REVERT: M 172 MET cc_start: 0.4283 (tpp) cc_final: 0.3910 (tpp) REVERT: M 194 ARG cc_start: 0.7388 (mpt-90) cc_final: 0.7001 (mpt-90) REVERT: M 195 MET cc_start: 0.4689 (ptm) cc_final: 0.3883 (ptm) REVERT: M 257 ILE cc_start: 0.7611 (mm) cc_final: 0.7300 (pt) REVERT: M 326 ASP cc_start: 0.5674 (t0) cc_final: 0.4896 (t0) REVERT: M 361 GLU cc_start: 0.9375 (mp0) cc_final: 0.8634 (tm-30) REVERT: O 37 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7618 (mm-30) REVERT: O 203 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7129 (p90) REVERT: O 405 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7674 (tm-30) REVERT: O 769 MET cc_start: 0.6854 (tpp) cc_final: 0.6558 (tpp) outliers start: 153 outliers final: 110 residues processed: 733 average time/residue: 0.4940 time to fit residues: 617.2107 Evaluate side-chains 677 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 557 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 373 ASP Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 626 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 672 ASN Chi-restraints excluded: chain G residue 686 LEU Chi-restraints excluded: chain G residue 704 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 718 ILE Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 TYR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain K residue 145 MET Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 301 VAL Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 704 LEU Chi-restraints excluded: chain L residue 716 ILE Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain N residue 234 TYR Chi-restraints excluded: chain N residue 244 PHE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 293 ILE Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 657 LEU Chi-restraints excluded: chain O residue 704 LEU Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 574 optimal weight: 0.9990 chunk 604 optimal weight: 8.9990 chunk 551 optimal weight: 7.9990 chunk 588 optimal weight: 0.7980 chunk 354 optimal weight: 7.9990 chunk 256 optimal weight: 0.5980 chunk 461 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 531 optimal weight: 3.9990 chunk 556 optimal weight: 0.7980 chunk 586 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 ASN ** G 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 146 GLN A 224 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 260 HIS ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 672 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 1.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 54528 Z= 0.189 Angle : 0.834 17.252 73695 Z= 0.386 Chirality : 0.047 0.230 8275 Planarity : 0.005 0.120 9300 Dihedral : 8.684 89.136 7561 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.24 % Favored : 90.60 % Rotamer: Outliers : 2.61 % Allowed : 21.47 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.22 % 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: -1.62 (0.10), residues: 6550 helix: 0.36 (0.10), residues: 2705 sheet: -1.59 (0.20), residues: 595 loop : -2.30 (0.11), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 203 HIS 0.011 0.001 HIS M 209 PHE 0.039 0.001 PHE M 207 TYR 0.041 0.001 TYR L 109 ARG 0.006 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 601 time to evaluate : 4.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 172 MET cc_start: 0.3150 (tpp) cc_final: 0.1403 (tpp) REVERT: I 178 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7640 (mm-30) REVERT: I 195 MET cc_start: 0.4472 (ptm) cc_final: 0.4113 (ptm) REVERT: I 257 ILE cc_start: 0.7326 (mm) cc_final: 0.6805 (pt) REVERT: I 287 LEU cc_start: 0.8936 (mt) cc_final: 0.8691 (tt) REVERT: I 361 GLU cc_start: 0.9390 (mp0) cc_final: 0.8627 (pp20) REVERT: H 202 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8276 (p0) REVERT: G 37 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7499 (mm-30) REVERT: G 203 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7172 (p90) REVERT: G 428 ASP cc_start: 0.7747 (p0) cc_final: 0.7313 (p0) REVERT: A 172 MET cc_start: 0.3748 (tpp) cc_final: 0.3333 (tpp) REVERT: A 177 LEU cc_start: 0.8977 (mm) cc_final: 0.8383 (pp) REVERT: A 195 MET cc_start: 0.4468 (OUTLIER) cc_final: 0.4024 (ptm) REVERT: A 257 ILE cc_start: 0.7750 (mm) cc_final: 0.7487 (pt) REVERT: A 361 GLU cc_start: 0.9493 (mp0) cc_final: 0.8949 (pp20) REVERT: B 141 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: B 301 MET cc_start: 0.8189 (mmm) cc_final: 0.7610 (mmm) REVERT: C 203 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6659 (p90) REVERT: C 405 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7632 (tm-30) REVERT: D 169 TYR cc_start: 0.6845 (m-10) cc_final: 0.6591 (m-80) REVERT: D 172 MET cc_start: 0.3333 (tpp) cc_final: 0.2084 (tpp) REVERT: D 195 MET cc_start: 0.4318 (ptt) cc_final: 0.3690 (ptm) REVERT: D 257 ILE cc_start: 0.7821 (mm) cc_final: 0.7527 (pt) REVERT: D 326 ASP cc_start: 0.5162 (t0) cc_final: 0.4512 (t0) REVERT: E 145 MET cc_start: 0.6956 (ppp) cc_final: 0.6695 (ppp) REVERT: E 301 MET cc_start: 0.8061 (mmm) cc_final: 0.7761 (mmm) REVERT: E 310 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8665 (tm) REVERT: F 203 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7221 (p90) REVERT: F 405 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7563 (tm-30) REVERT: F 765 MET cc_start: 0.7801 (ppp) cc_final: 0.7257 (ppp) REVERT: F 788 ASN cc_start: 0.7218 (p0) cc_final: 0.6641 (p0) REVERT: J 137 TRP cc_start: 0.7277 (t-100) cc_final: 0.6740 (t-100) REVERT: J 172 MET cc_start: 0.3630 (tpp) cc_final: 0.3188 (tpp) REVERT: J 195 MET cc_start: 0.4380 (ptm) cc_final: 0.3662 (ptm) REVERT: J 209 HIS cc_start: 0.7746 (m90) cc_final: 0.7212 (p90) REVERT: J 257 ILE cc_start: 0.7737 (mm) cc_final: 0.7455 (pt) REVERT: K 301 MET cc_start: 0.8123 (mmm) cc_final: 0.7678 (mmm) REVERT: L 203 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7186 (p90) REVERT: L 278 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7295 (p0) REVERT: L 405 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7512 (tm-30) REVERT: M 172 MET cc_start: 0.4255 (tpp) cc_final: 0.3902 (tpp) REVERT: M 194 ARG cc_start: 0.7414 (mpt-90) cc_final: 0.7040 (mpt-90) REVERT: M 195 MET cc_start: 0.4728 (ptm) cc_final: 0.3985 (ptm) REVERT: M 257 ILE cc_start: 0.7702 (mm) cc_final: 0.7466 (pt) REVERT: M 326 ASP cc_start: 0.5571 (t0) cc_final: 0.4781 (t0) REVERT: M 361 GLU cc_start: 0.9349 (mp0) cc_final: 0.8729 (pp20) REVERT: O 128 GLN cc_start: 0.8132 (pt0) cc_final: 0.7793 (pt0) REVERT: O 203 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7140 (p90) REVERT: O 346 ASP cc_start: 0.8408 (p0) cc_final: 0.8136 (p0) REVERT: O 769 MET cc_start: 0.6789 (tpp) cc_final: 0.6541 (tpp) outliers start: 155 outliers final: 111 residues processed: 713 average time/residue: 0.4815 time to fit residues: 588.6505 Evaluate side-chains 674 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 553 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 MET Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 373 ASP Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 672 ASN Chi-restraints excluded: chain G residue 686 LEU Chi-restraints excluded: chain G residue 704 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 718 ILE Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 TYR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 113 LYS Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 301 VAL Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 704 LEU Chi-restraints excluded: chain L residue 716 ILE Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain N residue 234 TYR Chi-restraints excluded: chain N residue 244 PHE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 293 ILE Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 560 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 657 LEU Chi-restraints excluded: chain O residue 704 LEU Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 386 optimal weight: 7.9990 chunk 622 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 432 optimal weight: 5.9990 chunk 652 optimal weight: 6.9990 chunk 600 optimal weight: 8.9990 chunk 519 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 401 optimal weight: 0.0020 chunk 318 optimal weight: 5.9990 overall best weight: 2.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 HIS ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 672 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 342 GLN F 377 HIS F 511 ASN F 595 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 511 ASN ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 1.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 54528 Z= 0.304 Angle : 0.865 17.641 73695 Z= 0.408 Chirality : 0.048 0.214 8275 Planarity : 0.005 0.120 9300 Dihedral : 8.735 88.763 7561 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.85 % Favored : 88.96 % Rotamer: Outliers : 2.46 % Allowed : 21.75 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -1.60 (0.10), residues: 6550 helix: 0.37 (0.10), residues: 2710 sheet: -1.49 (0.20), residues: 615 loop : -2.32 (0.11), residues: 3225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 203 HIS 0.017 0.001 HIS G 377 PHE 0.033 0.002 PHE M 207 TYR 0.013 0.001 TYR L 724 ARG 0.007 0.001 ARG G 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 546 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 172 MET cc_start: 0.3114 (tpp) cc_final: 0.1695 (tpp) REVERT: I 178 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7588 (mm-30) REVERT: I 257 ILE cc_start: 0.7429 (mm) cc_final: 0.7003 (pt) REVERT: I 361 GLU cc_start: 0.9411 (mp0) cc_final: 0.8663 (pp20) REVERT: H 202 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8292 (p0) REVERT: H 275 ASP cc_start: 0.9243 (t0) cc_final: 0.8643 (p0) REVERT: H 301 MET cc_start: 0.7849 (mmm) cc_final: 0.7514 (mmm) REVERT: G 37 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7356 (mm-30) REVERT: G 203 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7099 (p90) REVERT: G 428 ASP cc_start: 0.7791 (p0) cc_final: 0.7350 (p0) REVERT: A 172 MET cc_start: 0.3706 (tpp) cc_final: 0.3176 (tpp) REVERT: A 177 LEU cc_start: 0.9030 (mm) cc_final: 0.8463 (pp) REVERT: A 195 MET cc_start: 0.4838 (OUTLIER) cc_final: 0.4458 (ptm) REVERT: A 257 ILE cc_start: 0.7938 (mm) cc_final: 0.7738 (pt) REVERT: A 361 GLU cc_start: 0.9438 (mp0) cc_final: 0.8884 (pp20) REVERT: B 195 MET cc_start: 0.7728 (mmt) cc_final: 0.7488 (mmt) REVERT: B 202 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8790 (p0) REVERT: B 301 MET cc_start: 0.8252 (mmm) cc_final: 0.7713 (mmm) REVERT: C 203 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6817 (p90) REVERT: D 169 TYR cc_start: 0.6854 (m-10) cc_final: 0.6603 (m-80) REVERT: D 172 MET cc_start: 0.3411 (tpp) cc_final: 0.2245 (tpp) REVERT: D 177 LEU cc_start: 0.8832 (mm) cc_final: 0.8179 (pp) REVERT: D 195 MET cc_start: 0.4675 (ptt) cc_final: 0.4124 (ptm) REVERT: D 257 ILE cc_start: 0.8060 (mm) cc_final: 0.7853 (pt) REVERT: D 326 ASP cc_start: 0.5108 (t0) cc_final: 0.4463 (t0) REVERT: E 145 MET cc_start: 0.7287 (ppp) cc_final: 0.6975 (ppp) REVERT: E 301 MET cc_start: 0.7988 (mmm) cc_final: 0.7615 (mmm) REVERT: E 310 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8699 (tm) REVERT: F 405 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7686 (tm-30) REVERT: F 788 ASN cc_start: 0.7586 (p0) cc_final: 0.6959 (p0) REVERT: J 137 TRP cc_start: 0.7259 (t-100) cc_final: 0.6709 (t-100) REVERT: J 172 MET cc_start: 0.3766 (tpp) cc_final: 0.3346 (tpp) REVERT: J 195 MET cc_start: 0.4353 (ptm) cc_final: 0.3653 (ptm) REVERT: L 128 GLN cc_start: 0.7768 (mm110) cc_final: 0.7533 (mm-40) REVERT: L 203 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6834 (p90) REVERT: L 278 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7404 (p0) REVERT: L 405 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7698 (tm-30) REVERT: L 422 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8546 (mt) REVERT: M 172 MET cc_start: 0.4361 (tpp) cc_final: 0.3979 (tpp) REVERT: M 178 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8020 (tp30) REVERT: M 194 ARG cc_start: 0.7727 (mpt-90) cc_final: 0.7318 (mpt-90) REVERT: M 195 MET cc_start: 0.4867 (ptm) cc_final: 0.4221 (ptm) REVERT: M 326 ASP cc_start: 0.5760 (t0) cc_final: 0.4979 (t0) REVERT: M 361 GLU cc_start: 0.9356 (mp0) cc_final: 0.8715 (pp20) REVERT: O 203 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7245 (p90) REVERT: O 769 MET cc_start: 0.6930 (tpp) cc_final: 0.6631 (tpp) outliers start: 146 outliers final: 118 residues processed: 653 average time/residue: 0.4879 time to fit residues: 546.6369 Evaluate side-chains 653 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 525 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 MET Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 514 HIS Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 560 TYR Chi-restraints excluded: chain G residue 622 ASN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 686 LEU Chi-restraints excluded: chain G residue 704 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 716 ILE Chi-restraints excluded: chain G residue 718 ILE Chi-restraints excluded: chain G residue 736 THR Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 821 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 TYR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 TYR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 587 HIS Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 113 LYS Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 301 VAL Chi-restraints excluded: chain L residue 373 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 526 ILE Chi-restraints excluded: chain L residue 560 TYR Chi-restraints excluded: chain L residue 563 VAL Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 622 ASN Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 657 LEU Chi-restraints excluded: chain L residue 704 LEU Chi-restraints excluded: chain L residue 716 ILE Chi-restraints excluded: chain L residue 718 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain L residue 797 MET Chi-restraints excluded: chain L residue 821 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 218 VAL Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 293 ILE Chi-restraints excluded: chain O residue 321 ASP Chi-restraints excluded: chain O residue 373 ASP Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 526 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 587 HIS Chi-restraints excluded: chain O residue 622 ASN Chi-restraints excluded: chain O residue 642 THR Chi-restraints excluded: chain O residue 704 LEU Chi-restraints excluded: chain O residue 709 ASN Chi-restraints excluded: chain O residue 718 ILE Chi-restraints excluded: chain O residue 728 LEU Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 746 LEU Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 797 MET Chi-restraints excluded: chain O residue 821 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 412 optimal weight: 0.5980 chunk 553 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 479 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 520 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 534 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.066560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.048097 restraints weight = 268245.871| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 5.53 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 1.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.377 54528 Z= 0.366 Angle : 0.911 65.900 73695 Z= 0.448 Chirality : 0.048 0.304 8275 Planarity : 0.006 0.278 9300 Dihedral : 8.733 88.734 7561 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.87 % Favored : 88.95 % Rotamer: Outliers : 2.38 % Allowed : 21.82 % Favored : 75.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -1.60 (0.10), residues: 6550 helix: 0.38 (0.10), residues: 2705 sheet: -1.49 (0.20), residues: 615 loop : -2.32 (0.11), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 203 HIS 0.027 0.001 HIS L 377 PHE 0.024 0.002 PHE M 207 TYR 0.016 0.001 TYR F 27 ARG 0.005 0.000 ARG D 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12807.13 seconds wall clock time: 226 minutes 2.50 seconds (13562.50 seconds total)