Starting phenix.real_space_refine on Sun Jul 21 11:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/07_2024/6plq_20372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/07_2024/6plq_20372.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/07_2024/6plq_20372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/07_2024/6plq_20372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/07_2024/6plq_20372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/07_2024/6plq_20372.cif" } 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= 0.001 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9270 2.51 5 N 2290 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14240 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.64, per 1000 atoms: 0.61 Number of scatterers: 14240 At special positions: 0 Unit cell: (105.786, 107.745, 135.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2580 8.00 N 2290 7.00 C 9270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.19 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.19 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.19 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.19 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.19 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.5 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 39.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.233A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.234A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 245 through 256 removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.234A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.233A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 106 removed outlier: 4.040A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.233A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 228 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 227 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 228 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 227 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.565A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 228 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 227 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 228 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 227 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 165 through 167 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 228 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 227 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 165 through 167 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.790A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 565 hydrogen bonds defined for protein. 1635 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: 4.54 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4385 1.34 - 1.46: 3523 1.46 - 1.58: 6507 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 550 107.32 - 113.99: 8264 113.99 - 120.66: 5763 120.66 - 127.33: 5037 127.33 - 133.99: 161 Bond angle restraints: 19775 Sorted by residual: angle pdb=" CB ABU C 504 " pdb=" CG ABU C 504 " pdb=" CD ABU C 504 " ideal model delta sigma weight residual 116.08 109.39 6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB ABU B 504 " pdb=" CG ABU B 504 " pdb=" CD ABU B 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB ABU A 504 " pdb=" CG ABU A 504 " pdb=" CD ABU A 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" CB ABU D 504 " pdb=" CG ABU D 504 " pdb=" CD ABU D 504 " ideal model delta sigma weight residual 116.08 109.43 6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CB ABU E 504 " pdb=" CG ABU E 504 " pdb=" CD ABU E 504 " ideal model delta sigma weight residual 116.08 109.44 6.64 3.00e+00 1.11e-01 4.90e+00 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8725 21.75 - 43.50: 150 43.50 - 65.24: 5 65.24 - 86.99: 30 86.99 - 108.74: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.40 56.60 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2059 0.078 - 0.156: 196 0.156 - 0.235: 0 0.235 - 0.313: 5 0.313 - 0.391: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.82e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 103 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.016 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4025 2.81 - 3.33: 12257 3.33 - 3.85: 21913 3.85 - 4.38: 27100 4.38 - 4.90: 45477 Nonbonded interactions: 110772 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.286 2.440 ... (remaining 110767 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.260 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3725 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 : 0.002 0.027 14585 Z= 0.132 Angle : 0.526 6.685 19775 Z= 0.258 Chirality : 0.046 0.391 2265 Planarity : 0.003 0.028 2450 Dihedral : 11.125 108.738 5580 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.15), residues: 1710 helix: -4.20 (0.11), residues: 465 sheet: -2.53 (0.24), residues: 335 loop : -2.31 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 422 HIS 0.001 0.000 HIS C 125 PHE 0.003 0.001 PHE B 258 TYR 0.004 0.000 TYR D 74 ARG 0.002 0.000 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 1.548 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 outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3190 time to fit residues: 178.4814 Evaluate side-chains 240 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN B 62 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 131 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 131 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN E 62 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS E 131 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14585 Z= 0.328 Angle : 0.861 7.369 19775 Z= 0.432 Chirality : 0.052 0.204 2265 Planarity : 0.006 0.046 2450 Dihedral : 8.906 54.044 2200 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.35 % Allowed : 13.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.18), residues: 1710 helix: -2.31 (0.20), residues: 490 sheet: -2.07 (0.22), residues: 430 loop : -1.93 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 255 HIS 0.020 0.005 HIS E 125 PHE 0.041 0.003 PHE E 79 TYR 0.027 0.002 TYR C 144 ARG 0.006 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 279 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.4471 (t80) cc_final: 0.3902 (t80) REVERT: A 106 LEU cc_start: 0.3325 (OUTLIER) cc_final: 0.2772 (mm) REVERT: A 119 GLU cc_start: 0.3410 (OUTLIER) cc_final: 0.3062 (tt0) REVERT: A 171 GLN cc_start: 0.7511 (pt0) cc_final: 0.7204 (pm20) REVERT: B 60 PHE cc_start: 0.4385 (t80) cc_final: 0.3695 (t80) REVERT: B 106 LEU cc_start: 0.3755 (OUTLIER) cc_final: 0.3155 (mm) REVERT: B 163 MET cc_start: 0.6687 (mmm) cc_final: 0.6379 (mmm) REVERT: B 171 GLN cc_start: 0.7576 (pt0) cc_final: 0.7149 (pm20) REVERT: C 106 LEU cc_start: 0.3662 (OUTLIER) cc_final: 0.3210 (mm) REVERT: C 133 LEU cc_start: 0.5710 (tp) cc_final: 0.4899 (tt) REVERT: C 171 GLN cc_start: 0.7450 (pt0) cc_final: 0.7050 (pm20) REVERT: D 106 LEU cc_start: 0.3693 (OUTLIER) cc_final: 0.3085 (mm) REVERT: D 133 LEU cc_start: 0.5638 (tp) cc_final: 0.4922 (tt) REVERT: D 163 MET cc_start: 0.6712 (mmm) cc_final: 0.6440 (mmm) REVERT: D 171 GLN cc_start: 0.7530 (pt0) cc_final: 0.7159 (pm20) REVERT: E 106 LEU cc_start: 0.3398 (OUTLIER) cc_final: 0.2771 (mm) REVERT: E 171 GLN cc_start: 0.7601 (pt0) cc_final: 0.7136 (pm20) outliers start: 52 outliers final: 26 residues processed: 319 average time/residue: 0.2450 time to fit residues: 116.2644 Evaluate side-chains 228 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4820 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14585 Z= 0.183 Angle : 0.738 9.330 19775 Z= 0.354 Chirality : 0.046 0.194 2265 Planarity : 0.004 0.043 2450 Dihedral : 7.333 59.099 2200 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.48 % Allowed : 15.81 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.19), residues: 1710 helix: -1.21 (0.22), residues: 520 sheet: -1.64 (0.22), residues: 430 loop : -1.95 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 302 HIS 0.006 0.002 HIS E 217 PHE 0.025 0.002 PHE E 414 TYR 0.025 0.002 TYR A 317 ARG 0.004 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.0625 (OUTLIER) cc_final: -0.0198 (mt) REVERT: A 133 LEU cc_start: 0.6074 (tp) cc_final: 0.5467 (tt) REVERT: A 171 GLN cc_start: 0.7493 (pt0) cc_final: 0.7152 (pm20) REVERT: B 125 HIS cc_start: 0.3868 (m90) cc_final: 0.3601 (m90) REVERT: B 171 GLN cc_start: 0.7686 (pt0) cc_final: 0.7099 (pm20) REVERT: C 133 LEU cc_start: 0.6055 (tp) cc_final: 0.5526 (tt) REVERT: C 171 GLN cc_start: 0.7623 (pt0) cc_final: 0.7035 (pm20) REVERT: C 410 PHE cc_start: 0.6898 (m-10) cc_final: 0.6583 (m-80) REVERT: D 171 GLN cc_start: 0.7685 (pt0) cc_final: 0.7140 (pm20) REVERT: D 410 PHE cc_start: 0.6948 (m-10) cc_final: 0.6634 (m-80) REVERT: E 101 LEU cc_start: 0.1162 (OUTLIER) cc_final: 0.0573 (mt) REVERT: E 171 GLN cc_start: 0.7686 (pt0) cc_final: 0.7097 (pm20) REVERT: E 410 PHE cc_start: 0.6880 (m-10) cc_final: 0.6571 (m-80) outliers start: 54 outliers final: 36 residues processed: 251 average time/residue: 0.2185 time to fit residues: 84.6871 Evaluate side-chains 221 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 183 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5136 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14585 Z= 0.213 Angle : 0.733 11.264 19775 Z= 0.356 Chirality : 0.045 0.238 2265 Planarity : 0.004 0.036 2450 Dihedral : 5.631 42.535 2200 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.55 % Allowed : 17.55 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1710 helix: -0.63 (0.23), residues: 520 sheet: -1.31 (0.24), residues: 445 loop : -1.67 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.005 0.002 HIS B 217 PHE 0.017 0.002 PHE B 79 TYR 0.027 0.002 TYR D 175 ARG 0.005 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 212 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6808 (mmt) cc_final: 0.6311 (mmm) REVERT: A 171 GLN cc_start: 0.7896 (pt0) cc_final: 0.7145 (pm20) REVERT: B 163 MET cc_start: 0.6964 (mmm) cc_final: 0.6756 (mmm) REVERT: B 171 GLN cc_start: 0.7878 (pt0) cc_final: 0.7149 (pm20) REVERT: C 141 ASN cc_start: 0.6700 (m110) cc_final: 0.6326 (m-40) REVERT: C 163 MET cc_start: 0.7129 (mmm) cc_final: 0.6827 (mmm) REVERT: C 171 GLN cc_start: 0.7761 (pt0) cc_final: 0.6915 (pm20) REVERT: D 156 MET cc_start: 0.6835 (mmm) cc_final: 0.6430 (mmm) REVERT: D 171 GLN cc_start: 0.7898 (pt0) cc_final: 0.7150 (pm20) REVERT: E 171 GLN cc_start: 0.7741 (pt0) cc_final: 0.6888 (pm20) REVERT: E 418 ASN cc_start: 0.8753 (m-40) cc_final: 0.8325 (m110) outliers start: 55 outliers final: 35 residues processed: 260 average time/residue: 0.2204 time to fit residues: 88.8042 Evaluate side-chains 239 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 204 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 1.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 14585 Z= 0.402 Angle : 0.960 14.607 19775 Z= 0.482 Chirality : 0.051 0.241 2265 Planarity : 0.006 0.047 2450 Dihedral : 6.294 36.526 2200 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.71 % Allowed : 18.26 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1710 helix: -0.45 (0.24), residues: 515 sheet: -0.93 (0.26), residues: 425 loop : -1.26 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 84 HIS 0.021 0.005 HIS A 217 PHE 0.023 0.003 PHE B 29 TYR 0.062 0.003 TYR E 175 ARG 0.012 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.7669 (mmt) cc_final: 0.7305 (mmm) REVERT: A 171 GLN cc_start: 0.8313 (pt0) cc_final: 0.7406 (pm20) REVERT: A 242 GLN cc_start: 0.7655 (tt0) cc_final: 0.7377 (tm-30) REVERT: A 418 ASN cc_start: 0.9040 (m-40) cc_final: 0.8804 (m110) REVERT: B 34 MET cc_start: 0.6665 (ptt) cc_final: 0.6429 (ptt) REVERT: B 60 PHE cc_start: 0.4601 (t80) cc_final: 0.4353 (t80) REVERT: B 202 GLN cc_start: 0.8003 (pm20) cc_final: 0.7764 (pm20) REVERT: B 242 GLN cc_start: 0.7587 (tt0) cc_final: 0.7345 (tm-30) REVERT: C 24 MET cc_start: 0.3304 (ttt) cc_final: 0.2898 (ttt) REVERT: C 60 PHE cc_start: 0.4732 (t80) cc_final: 0.3996 (t80) REVERT: C 156 MET cc_start: 0.8264 (mmt) cc_final: 0.7997 (mmm) REVERT: C 218 TYR cc_start: 0.3999 (t80) cc_final: 0.3630 (t80) REVERT: C 242 GLN cc_start: 0.7584 (tt0) cc_final: 0.7342 (tm-30) REVERT: C 418 ASN cc_start: 0.9022 (m-40) cc_final: 0.8779 (m110) REVERT: D 82 GLN cc_start: 0.8235 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 133 LEU cc_start: 0.8018 (tt) cc_final: 0.7327 (tt) REVERT: D 142 VAL cc_start: 0.8064 (t) cc_final: 0.7541 (m) REVERT: D 151 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.7143 (m) REVERT: D 163 MET cc_start: 0.7646 (mmm) cc_final: 0.7434 (mmm) REVERT: D 418 ASN cc_start: 0.9020 (m-40) cc_final: 0.8766 (m110) REVERT: E 242 GLN cc_start: 0.7631 (tt0) cc_final: 0.7348 (tm-30) REVERT: E 418 ASN cc_start: 0.9090 (m-40) cc_final: 0.8809 (m110) outliers start: 73 outliers final: 44 residues processed: 337 average time/residue: 0.2115 time to fit residues: 110.8321 Evaluate side-chains 283 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN A 219 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 166 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 1.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 14585 Z= 0.413 Angle : 1.033 24.459 19775 Z= 0.510 Chirality : 0.054 0.274 2265 Planarity : 0.007 0.066 2450 Dihedral : 6.989 59.162 2200 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 5.68 % Allowed : 20.26 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1710 helix: -0.43 (0.23), residues: 505 sheet: -1.27 (0.23), residues: 430 loop : -1.37 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 186 HIS 0.030 0.006 HIS D 217 PHE 0.061 0.003 PHE A 79 TYR 0.018 0.002 TYR C 74 ARG 0.010 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 260 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8512 (pm20) cc_final: 0.8095 (pm20) REVERT: A 262 MET cc_start: 0.1706 (tpt) cc_final: 0.0807 (ttt) REVERT: B 151 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8184 (m) REVERT: C 24 MET cc_start: 0.5136 (ttt) cc_final: 0.4586 (ttt) REVERT: C 202 GLN cc_start: 0.8480 (pm20) cc_final: 0.7877 (pm20) REVERT: D 69 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7923 (mm-30) REVERT: D 202 GLN cc_start: 0.8101 (pm20) cc_final: 0.7741 (mp10) outliers start: 88 outliers final: 46 residues processed: 324 average time/residue: 0.2295 time to fit residues: 112.0364 Evaluate side-chains 267 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 418 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 1.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14585 Z= 0.342 Angle : 0.886 12.838 19775 Z= 0.430 Chirality : 0.048 0.231 2265 Planarity : 0.005 0.038 2450 Dihedral : 6.422 44.988 2200 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.74 % Allowed : 23.74 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1710 helix: -0.36 (0.23), residues: 515 sheet: -1.06 (0.25), residues: 405 loop : -0.99 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 84 HIS 0.009 0.002 HIS A 217 PHE 0.018 0.002 PHE E 29 TYR 0.019 0.002 TYR D 218 ARG 0.040 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.5275 (tmm) cc_final: 0.3594 (tmm) REVERT: A 79 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 202 GLN cc_start: 0.8615 (pm20) cc_final: 0.8172 (pm20) REVERT: A 242 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 262 MET cc_start: 0.1956 (tpt) cc_final: 0.1651 (mmm) REVERT: B 24 MET cc_start: 0.3963 (ttt) cc_final: 0.3110 (ttt) REVERT: B 242 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7132 (tm-30) REVERT: C 24 MET cc_start: 0.5898 (ttt) cc_final: 0.4481 (ttt) REVERT: C 105 MET cc_start: 0.5852 (tmm) cc_final: 0.5620 (tmm) REVERT: C 202 GLN cc_start: 0.8631 (pm20) cc_final: 0.8029 (pm20) REVERT: D 24 MET cc_start: 0.5310 (tmm) cc_final: 0.4876 (tmm) REVERT: E 130 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8216 (p0) outliers start: 58 outliers final: 40 residues processed: 275 average time/residue: 0.2148 time to fit residues: 91.7356 Evaluate side-chains 250 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN A 83 GLN C 83 GLN C 141 ASN C 166 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 1.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14585 Z= 0.206 Angle : 0.800 12.434 19775 Z= 0.378 Chirality : 0.046 0.238 2265 Planarity : 0.004 0.084 2450 Dihedral : 5.869 40.875 2200 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.23 % Allowed : 24.71 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1710 helix: -0.20 (0.23), residues: 530 sheet: -0.79 (0.25), residues: 430 loop : -1.40 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 84 HIS 0.006 0.001 HIS D 217 PHE 0.018 0.001 PHE A 29 TYR 0.016 0.001 TYR A 94 ARG 0.036 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7565 (t80) REVERT: A 202 GLN cc_start: 0.8592 (pm20) cc_final: 0.8158 (pm20) REVERT: A 262 MET cc_start: 0.2155 (tpt) cc_final: 0.1147 (mtp) REVERT: B 24 MET cc_start: 0.3239 (ttt) cc_final: 0.1698 (ttt) REVERT: B 241 ILE cc_start: 0.9207 (mp) cc_final: 0.8935 (mp) REVERT: C 24 MET cc_start: 0.5504 (ttt) cc_final: 0.3247 (ttt) REVERT: C 202 GLN cc_start: 0.8664 (pm20) cc_final: 0.8399 (pm20) REVERT: C 241 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8954 (mp) REVERT: D 24 MET cc_start: 0.5173 (tmm) cc_final: 0.3949 (tmm) REVERT: D 241 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8996 (mp) REVERT: E 130 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8015 (p0) REVERT: E 242 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7237 (tm-30) outliers start: 50 outliers final: 29 residues processed: 254 average time/residue: 0.2051 time to fit residues: 82.0658 Evaluate side-chains 238 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 141 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 1.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14585 Z= 0.193 Angle : 0.802 13.001 19775 Z= 0.376 Chirality : 0.046 0.228 2265 Planarity : 0.004 0.030 2450 Dihedral : 5.665 37.606 2200 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.71 % Allowed : 25.35 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1710 helix: -0.15 (0.23), residues: 520 sheet: -0.55 (0.25), residues: 430 loop : -1.20 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 84 HIS 0.004 0.001 HIS B 217 PHE 0.023 0.001 PHE C 60 TYR 0.014 0.001 TYR C 94 ARG 0.013 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.4707 (tmm) cc_final: 0.4458 (tmm) REVERT: A 79 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7631 (t80) REVERT: A 202 GLN cc_start: 0.8583 (pm20) cc_final: 0.8145 (pm20) REVERT: A 262 MET cc_start: 0.1998 (tpt) cc_final: 0.0989 (mtp) REVERT: B 59 ILE cc_start: 0.8873 (mp) cc_final: 0.8673 (mm) REVERT: B 241 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8866 (mp) REVERT: C 24 MET cc_start: 0.5300 (ttt) cc_final: 0.4582 (ttt) REVERT: C 202 GLN cc_start: 0.8663 (pm20) cc_final: 0.8391 (pm20) REVERT: C 241 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8904 (mp) REVERT: D 241 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8956 (mp) REVERT: E 130 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7938 (p0) REVERT: E 242 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7275 (tm-30) outliers start: 42 outliers final: 28 residues processed: 245 average time/residue: 0.2225 time to fit residues: 83.1515 Evaluate side-chains 233 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0770 chunk 76 optimal weight: 0.0980 chunk 112 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 0.2980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 1.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14585 Z= 0.185 Angle : 0.816 19.263 19775 Z= 0.379 Chirality : 0.046 0.228 2265 Planarity : 0.004 0.057 2450 Dihedral : 5.477 36.874 2200 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.65 % Allowed : 26.00 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1710 helix: -0.04 (0.24), residues: 520 sheet: -0.42 (0.26), residues: 420 loop : -1.24 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.005 0.001 HIS C 231 PHE 0.021 0.001 PHE A 115 TYR 0.017 0.001 TYR B 218 ARG 0.009 0.001 ARG A 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.4512 (tmm) cc_final: 0.4248 (tmm) REVERT: A 79 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7616 (t80) REVERT: A 202 GLN cc_start: 0.8581 (pm20) cc_final: 0.8153 (pm20) REVERT: A 262 MET cc_start: 0.2020 (tpt) cc_final: 0.1037 (mtp) REVERT: C 24 MET cc_start: 0.5171 (ttt) cc_final: 0.4783 (ttt) REVERT: C 202 GLN cc_start: 0.8670 (pm20) cc_final: 0.8339 (pm20) REVERT: C 241 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8867 (mp) REVERT: D 130 ASP cc_start: 0.8182 (p0) cc_final: 0.7741 (p0) REVERT: D 241 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8911 (mp) REVERT: E 130 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7913 (p0) REVERT: E 262 MET cc_start: 0.1043 (tpt) cc_final: 0.0768 (mmm) outliers start: 41 outliers final: 27 residues processed: 241 average time/residue: 0.2128 time to fit residues: 79.5853 Evaluate side-chains 233 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.101569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077239 restraints weight = 50453.076| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 6.40 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 1.7837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 14585 Z= 0.283 Angle : 0.894 13.627 19775 Z= 0.434 Chirality : 0.048 0.217 2265 Planarity : 0.005 0.062 2450 Dihedral : 5.787 30.376 2200 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.45 % Allowed : 26.84 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1710 helix: -0.30 (0.23), residues: 530 sheet: -0.25 (0.29), residues: 340 loop : -1.21 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 110 HIS 0.009 0.002 HIS B 217 PHE 0.024 0.002 PHE C 60 TYR 0.022 0.002 TYR B 218 ARG 0.015 0.001 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.08 seconds wall clock time: 54 minutes 35.96 seconds (3275.96 seconds total)