Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 20:38:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_0680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_0680.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_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_0680/10_2023/6j5t_0680_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_0680_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_0680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_0680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_0680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5t_0680/10_2023/6j5t_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 19.90, 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: 16.00 Conformation dependent library (CDL) restraints added in 5.9 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: 7.91 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: 14.81 Time building geometry restraints manager: 17.52 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=" C3 BQL D 501 " pdb=" C3' BQL D 501 " ideal model delta sigma weight residual 1.297 1.519 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3 BQL J 501 " pdb=" C3' BQL J 501 " ideal model delta sigma weight residual 1.297 1.519 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3 BQL I 501 " pdb=" C3' BQL I 501 " ideal model delta sigma weight residual 1.297 1.518 -0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3 BQL M 501 " pdb=" C3' BQL M 501 " ideal model delta sigma weight residual 1.297 1.518 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C3 BQL A 501 " pdb=" C3' BQL A 501 " ideal model delta sigma weight residual 1.297 1.517 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (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 - 34.29: 32555 34.29 - 68.59: 424 68.59 - 102.88: 53 102.88 - 137.17: 9 137.17 - 171.47: 5 Dihedral angle restraints: 33046 sinusoidal: 13756 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 33043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 6598 0.081 - 0.161: 1467 0.161 - 0.242: 150 0.242 - 0.322: 30 0.322 - 0.403: 5 Chirality restraints: 8250 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 8247 not shown) Planarity restraints: 9315 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 9312 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: 2.680 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.190 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 101.690 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.880 ------------------------------------------------------------------------------- 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 : 0.011 0.222 54528 Z= 0.733 Angle : 1.209 14.104 73695 Z= 0.655 Chirality : 0.066 0.403 8250 Planarity : 0.017 0.486 9305 Dihedral : 12.809 171.466 20526 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 *********************** 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 : 4.760 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 outliers start: 35 outliers final: 8 residues processed: 1779 average time/residue: 0.5376 time to fit residues: 1558.2713 Evaluate side-chains 994 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 986 time to evaluate : 4.818 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3797 time to fit residues: 12.1312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 553 optimal weight: 3.9990 chunk 496 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 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: 1.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 180 HIS E 189 HIS E 311 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 601 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 54528 Z= 0.228 Angle : 0.965 19.974 73695 Z= 0.440 Chirality : 0.048 0.293 8250 Planarity : 0.006 0.089 9305 Dihedral : 11.797 179.819 7346 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.25 % Favored : 90.44 % Rotamer: Outliers : 3.44 % Allowed : 15.03 % Favored : 81.53 % 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: -3.05 (0.10), residues: 6550 helix: -1.05 (0.09), residues: 2730 sheet: -2.52 (0.19), residues: 630 loop : -2.84 (0.10), residues: 3190 *********************** 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 1265 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1061 time to evaluate : 4.803 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 outliers start: 204 outliers final: 71 residues processed: 1201 average time/residue: 0.5092 time to fit residues: 1026.5431 Evaluate side-chains 939 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 868 time to evaluate : 4.785 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3952 time to fit residues: 58.4024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 330 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 495 optimal weight: 0.9990 chunk 405 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 595 optimal weight: 10.0000 chunk 643 optimal weight: 4.9990 chunk 530 optimal weight: 5.9990 chunk 590 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 478 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 117 HIS ** 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 236 ASN G 255 GLN ** G 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 812 GLN A 179 ASN A 209 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN C 255 GLN C 438 HIS ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 GLN C 812 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 117 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN F 438 HIS F 747 GLN F 780 GLN F 812 GLN J 142 ASN J 179 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 L 228 GLN L 255 GLN L 434 GLN ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 ASN ** 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 812 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 54528 Z= 0.370 Angle : 1.015 19.903 73695 Z= 0.479 Chirality : 0.051 0.237 8250 Planarity : 0.007 0.096 9305 Dihedral : 10.916 178.873 7346 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.85 % Favored : 88.84 % Rotamer: Outliers : 3.88 % Allowed : 16.07 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.44 % 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: -2.57 (0.10), residues: 6550 helix: -0.47 (0.10), residues: 2740 sheet: -2.52 (0.18), residues: 675 loop : -2.69 (0.10), residues: 3135 *********************** 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 1075 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 845 time to evaluate : 4.811 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 outliers start: 230 outliers final: 98 residues processed: 1029 average time/residue: 0.5031 time to fit residues: 873.6651 Evaluate side-chains 747 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 649 time to evaluate : 4.855 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.3941 time to fit residues: 78.0762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 588 optimal weight: 0.9990 chunk 448 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 284 optimal weight: 0.0020 chunk 400 optimal weight: 0.9990 chunk 598 optimal weight: 0.8980 chunk 633 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 566 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 151 ASN ** I 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN B 122 GLN C 525 GLN C 595 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 GLN ** D 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 209 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 HIS L 228 GLN ** L 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 709 ASN ** O 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 54528 Z= 0.184 Angle : 0.903 18.021 73695 Z= 0.406 Chirality : 0.047 0.250 8250 Planarity : 0.005 0.077 9305 Dihedral : 10.589 179.348 7346 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.61 % Favored : 91.13 % Rotamer: Outliers : 2.41 % Allowed : 18.45 % Favored : 79.14 % 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: -2.13 (0.10), residues: 6550 helix: -0.02 (0.10), residues: 2720 sheet: -2.24 (0.19), residues: 635 loop : -2.54 (0.10), residues: 3195 *********************** 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 919 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 776 time to evaluate : 5.046 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 outliers start: 143 outliers final: 43 residues processed: 888 average time/residue: 0.5166 time to fit residues: 771.1643 Evaluate side-chains 717 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 674 time to evaluate : 4.848 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3796 time to fit residues: 37.4335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 527 optimal weight: 10.0000 chunk 359 optimal weight: 0.0870 chunk 9 optimal weight: 9.9990 chunk 471 optimal weight: 5.9990 chunk 261 optimal weight: 0.0970 chunk 540 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 323 optimal weight: 4.9990 chunk 568 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.4362 ------------------------------------------------------------------------------- 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** ** I 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN G 322 ASN G 385 HIS G 434 GLN G 525 GLN ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 780 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** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 GLN F 322 ASN K 122 GLN L 236 ASN L 322 ASN ** 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 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 322 ASN O 434 GLN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 747 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.8377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 54528 Z= 0.282 Angle : 0.906 17.283 73695 Z= 0.415 Chirality : 0.047 0.281 8250 Planarity : 0.005 0.098 9305 Dihedral : 10.300 179.693 7346 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.58 % Favored : 89.15 % Rotamer: Outliers : 2.33 % Allowed : 19.46 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.20 % 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: -1.99 (0.10), residues: 6550 helix: 0.04 (0.10), residues: 2755 sheet: -2.11 (0.19), residues: 635 loop : -2.46 (0.10), residues: 3160 *********************** 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 844 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 706 time to evaluate : 4.920 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 outliers start: 138 outliers final: 65 residues processed: 798 average time/residue: 0.5225 time to fit residues: 704.2948 Evaluate side-chains 685 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 620 time to evaluate : 4.831 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4338 time to fit residues: 57.9453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 213 optimal weight: 0.2980 chunk 570 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 371 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 633 optimal weight: 0.0670 chunk 526 optimal weight: 0.5980 chunk 293 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 332 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** ** I 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 ASN A 142 ASN 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** D 209 HIS D 332 GLN F 511 ASN J 179 ASN ** 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** M 142 ASN M 332 GLN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.8620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54528 Z= 0.179 Angle : 0.892 17.275 73695 Z= 0.397 Chirality : 0.046 0.360 8250 Planarity : 0.004 0.074 9305 Dihedral : 10.011 178.850 7346 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.55 % Favored : 91.25 % Rotamer: Outliers : 1.60 % Allowed : 20.00 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.10), residues: 6550 helix: 0.26 (0.10), residues: 2725 sheet: -2.04 (0.19), residues: 635 loop : -2.41 (0.10), residues: 3190 *********************** 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 823 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 728 time to evaluate : 5.402 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 outliers start: 95 outliers final: 40 residues processed: 794 average time/residue: 0.5128 time to fit residues: 684.8698 Evaluate side-chains 675 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 635 time to evaluate : 4.789 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3757 time to fit residues: 35.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 611 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 462 optimal weight: 0.7980 chunk 358 optimal weight: 4.9990 chunk 533 optimal weight: 20.0000 chunk 353 optimal weight: 0.6980 chunk 631 optimal weight: 3.9990 chunk 395 optimal weight: 6.9990 chunk 384 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 142 HIS ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** C 595 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** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 ASN J 179 ASN ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.9244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54528 Z= 0.228 Angle : 0.898 17.335 73695 Z= 0.402 Chirality : 0.047 0.301 8250 Planarity : 0.005 0.091 9305 Dihedral : 9.807 179.930 7346 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.29 % Favored : 89.53 % Rotamer: Outliers : 1.58 % Allowed : 20.42 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.16 % 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: -1.75 (0.10), residues: 6550 helix: 0.26 (0.10), residues: 2750 sheet: -2.00 (0.19), residues: 680 loop : -2.33 (0.11), residues: 3120 *********************** 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 754 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 660 time to evaluate : 4.998 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 outliers start: 94 outliers final: 42 residues processed: 715 average time/residue: 0.5192 time to fit residues: 626.5373 Evaluate side-chains 645 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 603 time to evaluate : 4.838 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4075 time to fit residues: 37.8064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 390 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 377 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 401 optimal weight: 30.0000 chunk 430 optimal weight: 9.9990 chunk 312 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 496 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 332 GLN ** C 595 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** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN F 511 ASN ** F 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 780 GLN J 179 ASN ** 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** N 142 HIS ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 595 ASN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.9567 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= 0.196 Angle : 0.894 17.252 73695 Z= 0.398 Chirality : 0.046 0.289 8250 Planarity : 0.004 0.073 9305 Dihedral : 9.685 179.855 7346 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.08 % Favored : 90.75 % Rotamer: Outliers : 0.91 % Allowed : 21.23 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.10), residues: 6550 helix: 0.27 (0.10), residues: 2760 sheet: -1.72 (0.20), residues: 630 loop : -2.32 (0.11), residues: 3160 *********************** 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 704 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 650 time to evaluate : 5.251 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 outliers start: 54 outliers final: 18 residues processed: 688 average time/residue: 0.5224 time to fit residues: 603.9865 Evaluate side-chains 605 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 587 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3701 time to fit residues: 19.2438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 574 optimal weight: 0.9980 chunk 604 optimal weight: 10.0000 chunk 551 optimal weight: 5.9990 chunk 588 optimal weight: 2.9990 chunk 354 optimal weight: 0.5980 chunk 256 optimal weight: 0.1980 chunk 461 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 531 optimal weight: 7.9990 chunk 556 optimal weight: 8.9990 chunk 586 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 146 GLN B 142 HIS C 511 ASN ** C 595 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** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN ** F 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 780 GLN ** 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 595 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: 0.7971 moved from start: 0.9891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54528 Z= 0.191 Angle : 0.906 17.414 73695 Z= 0.402 Chirality : 0.046 0.277 8250 Planarity : 0.004 0.070 9305 Dihedral : 9.594 177.434 7346 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.56 % Favored : 90.29 % Rotamer: Outliers : 0.54 % Allowed : 21.97 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % 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: -1.59 (0.10), residues: 6550 helix: 0.35 (0.10), residues: 2750 sheet: -1.60 (0.20), residues: 630 loop : -2.28 (0.11), residues: 3170 *********************** 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 668 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 636 time to evaluate : 4.984 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 outliers start: 32 outliers final: 13 residues processed: 654 average time/residue: 0.5209 time to fit residues: 573.6170 Evaluate side-chains 606 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 593 time to evaluate : 4.841 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4334 time to fit residues: 16.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 386 optimal weight: 1.9990 chunk 622 optimal weight: 0.3980 chunk 379 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 432 optimal weight: 6.9990 chunk 652 optimal weight: 0.8980 chunk 600 optimal weight: 3.9990 chunk 519 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 401 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 405 GLN ** C 595 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** ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS F 511 ASN F 595 ASN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 332 GLN ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 780 GLN ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 1.0287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54528 Z= 0.201 Angle : 0.915 17.250 73695 Z= 0.406 Chirality : 0.046 0.267 8250 Planarity : 0.004 0.065 9305 Dihedral : 9.556 176.953 7346 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 0.44 % Allowed : 22.51 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.17 % 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: -1.58 (0.10), residues: 6550 helix: 0.40 (0.10), residues: 2750 sheet: -1.74 (0.20), residues: 680 loop : -2.28 (0.11), residues: 3120 ********************** 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 675 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 649 time to evaluate : 4.899 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 outliers start: 26 outliers final: 11 residues processed: 664 average time/residue: 0.5125 time to fit residues: 576.9471 Evaluate side-chains 597 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 586 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3832 time to fit residues: 14.5052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 412 optimal weight: 10.0000 chunk 553 optimal weight: 0.0040 chunk 159 optimal weight: 6.9990 chunk 479 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 520 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 534 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 3.5998 ------------------------------------------------------------------------------- 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 189 HIS ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** C 595 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** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN J 260 HIS K 117 HIS L 128 GLN L 377 HIS L 525 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** N 180 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 525 GLN ** O 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.066373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048320 restraints weight = 270138.423| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 5.00 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 1.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 54528 Z= 0.378 Angle : 1.005 18.257 73695 Z= 0.465 Chirality : 0.050 0.279 8250 Planarity : 0.005 0.088 9305 Dihedral : 9.845 178.939 7346 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.28 % Favored : 88.49 % Rotamer: Outliers : 0.69 % Allowed : 22.43 % Favored : 76.88 % 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: -1.87 (0.10), residues: 6550 helix: 0.20 (0.10), residues: 2720 sheet: -1.96 (0.19), residues: 735 loop : -2.43 (0.11), residues: 3095 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12553.32 seconds wall clock time: 222 minutes 21.78 seconds (13341.78 seconds total)