Starting phenix.real_space_refine on Fri Feb 16 23:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1m_21512/02_2024/6w1m_21512_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1m_21512/02_2024/6w1m_21512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1m_21512/02_2024/6w1m_21512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1m_21512/02_2024/6w1m_21512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1m_21512/02_2024/6w1m_21512_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1m_21512/02_2024/6w1m_21512_neut_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 11105 2.51 5 N 2710 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 439": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16885 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3260 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3260 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3260 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3260 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3260 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S87': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S87': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S87': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S87': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S87': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.26, per 1000 atoms: 0.55 Number of scatterers: 16885 At special positions: 0 Unit cell: (103.456, 106, 172.992, 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 50 16.00 O 3020 8.00 N 2710 7.00 C 11105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG H 1 " - " ASN A 148 " " NAG K 1 " - " ASN B 148 " " NAG N 1 " - " ASN C 148 " " NAG Q 1 " - " ASN D 148 " " NAG T 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 2.9 seconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 20 sheets defined 37.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.688A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 175' Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.755A pdb=" N ALA A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.963A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 272 removed outlier: 3.555A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.536A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 398 through 414 removed outlier: 3.669A pdb=" N LEU A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 460 removed outlier: 4.317A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.687A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 175' Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.755A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 removed outlier: 3.963A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 272 removed outlier: 3.556A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.537A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 398 through 414 removed outlier: 3.669A pdb=" N LEU B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 460 removed outlier: 4.317A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.687A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 175' Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.754A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 239 removed outlier: 3.963A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 272 removed outlier: 3.555A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 307 removed outlier: 3.535A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 398 through 414 removed outlier: 3.669A pdb=" N LEU C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 460 removed outlier: 4.316A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.687A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 175' Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.755A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 239 removed outlier: 3.964A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 272 removed outlier: 3.556A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 307 removed outlier: 3.535A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.670A pdb=" N LEU D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 460 removed outlier: 4.317A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.688A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.754A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 239 removed outlier: 3.963A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 272 removed outlier: 3.555A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 258 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.536A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.669A pdb=" N LEU E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 460 removed outlier: 4.317A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.314A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 131 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.313A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 131 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.313A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 131 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.313A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 131 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.313A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 131 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.155A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1785 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: 4.56 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4838 1.33 - 1.45: 3170 1.45 - 1.57: 9267 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17350 Sorted by residual: bond pdb=" C06 S87 B 508 " pdb=" O01 S87 B 508 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" C06 S87 E 508 " pdb=" O01 S87 E 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C06 S87 C 508 " pdb=" O01 S87 C 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C06 S87 D 508 " pdb=" O01 S87 D 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" C06 S87 A 508 " pdb=" O01 S87 A 508 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 6.97e+01 ... (remaining 17345 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.40: 290 104.40 - 112.70: 9370 112.70 - 120.99: 9126 120.99 - 129.29: 4714 129.29 - 137.58: 215 Bond angle restraints: 23715 Sorted by residual: angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 137.58 -30.29 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 137.54 -30.25 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " pdb=" O4 NAG T 1 " ideal model delta sigma weight residual 107.29 137.50 -30.21 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C3 NAG K 1 " pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 107.29 137.49 -30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C3 NAG Q 1 " pdb=" C4 NAG Q 1 " pdb=" O4 NAG Q 1 " ideal model delta sigma weight residual 107.29 137.47 -30.18 3.00e+00 1.11e-01 1.01e+02 ... (remaining 23710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10040 21.43 - 42.86: 475 42.86 - 64.29: 80 64.29 - 85.71: 30 85.71 - 107.14: 20 Dihedral angle restraints: 10645 sinusoidal: 4765 harmonic: 5880 Sorted by residual: dihedral pdb=" CA ILE A 41 " pdb=" C ILE A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE E 41 " pdb=" C ILE E 41 " pdb=" N ASP E 42 " pdb=" CA ASP E 42 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE B 41 " pdb=" C ILE B 41 " pdb=" N ASP B 42 " pdb=" CA ASP B 42 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 10642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.527: 2805 0.527 - 1.055: 0 1.055 - 1.582: 5 1.582 - 2.110: 0 2.110 - 2.637: 10 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C4 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" C5 NAG Q 1 " pdb=" O4 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.53 0.11 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C4 NAG T 1 " pdb=" C3 NAG T 1 " pdb=" C5 NAG T 1 " pdb=" O4 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.53 0.11 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C4 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C5 NAG K 1 " pdb=" O4 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.53 0.11 -2.64 2.00e-01 2.50e+01 1.74e+02 ... (remaining 2817 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " 0.023 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP D 168 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.023 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP A 168 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " 0.023 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP C 168 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.008 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5067 2.83 - 3.35: 14303 3.35 - 3.86: 26632 3.86 - 4.38: 29842 4.38 - 4.90: 50955 Nonbonded interactions: 126799 Sorted by model distance: nonbonded pdb=" O4 NAG O 1 " pdb=" O3 NAG O 2 " model vdw 2.309 2.432 nonbonded pdb=" O4 NAG L 1 " pdb=" O3 NAG L 2 " model vdw 2.309 2.432 nonbonded pdb=" O4 NAG F 1 " pdb=" O3 NAG F 2 " model vdw 2.309 2.432 nonbonded pdb=" O4 NAG I 1 " pdb=" O3 NAG I 2 " model vdw 2.310 2.432 nonbonded pdb=" O4 NAG R 1 " pdb=" O3 NAG R 2 " model vdw 2.310 2.432 ... (remaining 126794 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' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'H' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'I' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'K' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'L' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'N' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'O' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'Q' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'R' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'T' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 6.440 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 45.510 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.168 17350 Z= 0.659 Angle : 1.268 30.290 23715 Z= 0.585 Chirality : 0.173 2.637 2820 Planarity : 0.006 0.044 2855 Dihedral : 14.389 107.142 6815 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.27 % Allowed : 8.99 % Favored : 90.74 % 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: -5.48 (0.13), residues: 1950 helix: -4.49 (0.07), residues: 750 sheet: -2.09 (0.22), residues: 395 loop : -3.40 (0.17), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP D 168 HIS 0.005 0.002 HIS B 309 PHE 0.021 0.003 PHE B 72 TYR 0.025 0.002 TYR D 67 ARG 0.014 0.001 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 300 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8563 (mmpt) cc_final: 0.8290 (ptmm) REVERT: A 268 ILE cc_start: 0.9102 (tp) cc_final: 0.8901 (tt) REVERT: A 311 GLN cc_start: 0.6625 (pm20) cc_final: 0.6244 (pm20) REVERT: A 313 LEU cc_start: 0.6972 (pt) cc_final: 0.6564 (pt) REVERT: A 411 HIS cc_start: 0.9036 (t70) cc_final: 0.8802 (t70) REVERT: B 267 ILE cc_start: 0.8711 (mt) cc_final: 0.8470 (pt) REVERT: B 311 GLN cc_start: 0.6626 (pm20) cc_final: 0.6384 (pm20) REVERT: B 313 LEU cc_start: 0.7246 (pt) cc_final: 0.6678 (pt) REVERT: B 314 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7768 (pt0) REVERT: B 411 HIS cc_start: 0.8991 (t70) cc_final: 0.8770 (t70) REVERT: B 417 ASP cc_start: 0.8604 (p0) cc_final: 0.8221 (t0) REVERT: C 264 VAL cc_start: 0.8230 (t) cc_final: 0.8024 (t) REVERT: C 267 ILE cc_start: 0.8772 (mt) cc_final: 0.8518 (pt) REVERT: C 311 GLN cc_start: 0.6439 (pm20) cc_final: 0.6168 (pm20) REVERT: C 314 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7693 (mm-40) REVERT: C 411 HIS cc_start: 0.8864 (t70) cc_final: 0.8508 (t-90) REVERT: C 417 ASP cc_start: 0.8690 (p0) cc_final: 0.8314 (t0) REVERT: D 311 GLN cc_start: 0.6258 (pm20) cc_final: 0.5885 (pm20) REVERT: D 314 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7654 (pt0) REVERT: D 411 HIS cc_start: 0.8832 (t70) cc_final: 0.8478 (t-90) REVERT: D 417 ASP cc_start: 0.8570 (p0) cc_final: 0.8227 (t0) REVERT: E 311 GLN cc_start: 0.6483 (pm20) cc_final: 0.5951 (pm20) REVERT: E 313 LEU cc_start: 0.7263 (pt) cc_final: 0.6810 (pt) REVERT: E 411 HIS cc_start: 0.8951 (t70) cc_final: 0.8713 (t70) REVERT: E 417 ASP cc_start: 0.8689 (p0) cc_final: 0.8329 (t0) REVERT: E 434 ASP cc_start: 0.8261 (t70) cc_final: 0.8014 (t0) outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.3588 time to fit residues: 150.1997 Evaluate side-chains 195 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 205 ASN B 82 ASN B 183 ASN B 205 ASN C 82 ASN C 183 ASN D 82 ASN E 82 ASN E 205 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17350 Z= 0.231 Angle : 0.777 13.195 23715 Z= 0.363 Chirality : 0.053 0.380 2820 Planarity : 0.005 0.042 2855 Dihedral : 11.392 67.490 2950 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.60 % Allowed : 11.01 % Favored : 85.40 % 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: -3.62 (0.16), residues: 1950 helix: -2.03 (0.16), residues: 755 sheet: -2.31 (0.19), residues: 495 loop : -2.58 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 168 HIS 0.003 0.001 HIS C 460 PHE 0.012 0.001 PHE A 412 TYR 0.019 0.002 TYR D 448 ARG 0.010 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 210 time to evaluate : 1.958 Fit side-chains REVERT: A 320 TRP cc_start: 0.7320 (m-10) cc_final: 0.7023 (m-10) REVERT: A 411 HIS cc_start: 0.9047 (t70) cc_final: 0.8840 (t70) REVERT: B 180 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8695 (pp) REVERT: B 411 HIS cc_start: 0.8997 (t70) cc_final: 0.8747 (t-90) REVERT: B 417 ASP cc_start: 0.8420 (p0) cc_final: 0.8104 (t0) REVERT: C 180 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8547 (pp) REVERT: C 411 HIS cc_start: 0.8910 (t70) cc_final: 0.8637 (t-90) REVERT: C 417 ASP cc_start: 0.8391 (p0) cc_final: 0.8069 (p0) REVERT: C 443 LEU cc_start: 0.8661 (mt) cc_final: 0.8290 (tt) REVERT: D 141 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7631 (p0) REVERT: D 311 GLN cc_start: 0.6121 (pm20) cc_final: 0.5888 (pm20) REVERT: D 317 VAL cc_start: 0.7904 (t) cc_final: 0.7056 (m) REVERT: E 310 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7983 (mtpp) REVERT: E 311 GLN cc_start: 0.6348 (pm20) cc_final: 0.5962 (pm20) REVERT: E 314 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: E 434 ASP cc_start: 0.8159 (t70) cc_final: 0.7893 (t0) outliers start: 66 outliers final: 26 residues processed: 265 average time/residue: 0.2669 time to fit residues: 108.0691 Evaluate side-chains 186 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 157 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 101 ASN D 101 ASN D 183 ASN D 184 GLN E 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17350 Z= 0.201 Angle : 0.683 12.216 23715 Z= 0.318 Chirality : 0.049 0.407 2820 Planarity : 0.004 0.033 2855 Dihedral : 9.721 55.725 2950 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.36 % Allowed : 11.83 % Favored : 83.81 % 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: -2.69 (0.17), residues: 1950 helix: -0.81 (0.18), residues: 740 sheet: -2.08 (0.20), residues: 470 loop : -2.44 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 320 HIS 0.002 0.000 HIS A 460 PHE 0.010 0.001 PHE C 412 TYR 0.016 0.001 TYR A 448 ARG 0.005 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 181 time to evaluate : 1.989 Fit side-chains revert: symmetry clash REVERT: A 320 TRP cc_start: 0.7308 (m-10) cc_final: 0.7040 (m-10) REVERT: A 411 HIS cc_start: 0.9033 (t70) cc_final: 0.8792 (t-90) REVERT: B 103 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: B 180 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8728 (pp) REVERT: B 411 HIS cc_start: 0.8974 (t70) cc_final: 0.8742 (t-90) REVERT: C 180 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8544 (pp) REVERT: C 320 TRP cc_start: 0.7280 (m-10) cc_final: 0.7069 (m-10) REVERT: C 411 HIS cc_start: 0.8904 (t70) cc_final: 0.8637 (t70) REVERT: C 443 LEU cc_start: 0.8583 (mt) cc_final: 0.8289 (tt) REVERT: D 141 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7595 (p0) REVERT: D 180 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8776 (pp) REVERT: D 311 GLN cc_start: 0.6227 (pm20) cc_final: 0.5974 (pm20) REVERT: E 310 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7975 (mtpp) REVERT: E 311 GLN cc_start: 0.6413 (pm20) cc_final: 0.6129 (pm20) outliers start: 80 outliers final: 34 residues processed: 252 average time/residue: 0.2665 time to fit residues: 102.9097 Evaluate side-chains 193 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 0.0070 chunk 93 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17350 Z= 0.270 Angle : 0.679 11.691 23715 Z= 0.321 Chirality : 0.050 0.402 2820 Planarity : 0.004 0.038 2855 Dihedral : 8.091 56.843 2950 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.03 % Allowed : 13.68 % Favored : 82.29 % 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: -1.95 (0.18), residues: 1950 helix: 0.17 (0.19), residues: 740 sheet: -1.89 (0.20), residues: 460 loop : -2.30 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 456 HIS 0.002 0.001 HIS B 460 PHE 0.016 0.002 PHE B 153 TYR 0.013 0.001 TYR D 448 ARG 0.020 0.001 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 174 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 268 ILE cc_start: 0.8973 (tp) cc_final: 0.8756 (tt) REVERT: A 320 TRP cc_start: 0.7263 (m-10) cc_final: 0.7026 (m-10) REVERT: A 411 HIS cc_start: 0.8987 (t70) cc_final: 0.8759 (t-90) REVERT: A 417 ASP cc_start: 0.8389 (p0) cc_final: 0.7820 (p0) REVERT: B 103 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8667 (m-10) REVERT: C 180 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8614 (pp) REVERT: C 320 TRP cc_start: 0.7299 (m-10) cc_final: 0.7029 (m-10) REVERT: C 328 ARG cc_start: 0.6880 (mmp80) cc_final: 0.5567 (mmp80) REVERT: C 411 HIS cc_start: 0.8888 (t70) cc_final: 0.8649 (t70) REVERT: C 417 ASP cc_start: 0.8191 (p0) cc_final: 0.7904 (p0) REVERT: C 443 LEU cc_start: 0.8584 (mt) cc_final: 0.8308 (tt) REVERT: D 141 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7607 (p0) REVERT: D 180 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8801 (pp) REVERT: D 311 GLN cc_start: 0.6297 (pm20) cc_final: 0.6029 (pm20) REVERT: E 311 GLN cc_start: 0.6460 (pm20) cc_final: 0.6194 (pm20) REVERT: E 322 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8265 (tpp80) outliers start: 74 outliers final: 46 residues processed: 237 average time/residue: 0.2826 time to fit residues: 102.0841 Evaluate side-chains 199 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.0970 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17350 Z= 0.266 Angle : 0.666 11.334 23715 Z= 0.313 Chirality : 0.049 0.394 2820 Planarity : 0.004 0.051 2855 Dihedral : 7.616 56.666 2950 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.76 % Allowed : 14.93 % Favored : 81.31 % 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: -1.51 (0.19), residues: 1950 helix: 0.76 (0.20), residues: 740 sheet: -1.78 (0.20), residues: 460 loop : -2.24 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 320 HIS 0.009 0.001 HIS B 411 PHE 0.019 0.001 PHE A 233 TYR 0.013 0.001 TYR C 67 ARG 0.008 0.001 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 163 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: A 268 ILE cc_start: 0.8963 (tp) cc_final: 0.8745 (tt) REVERT: A 320 TRP cc_start: 0.7261 (m-10) cc_final: 0.7006 (m-10) REVERT: A 417 ASP cc_start: 0.8371 (p0) cc_final: 0.7842 (p0) REVERT: B 103 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8653 (m-10) REVERT: C 180 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8667 (pp) REVERT: C 320 TRP cc_start: 0.7282 (m-10) cc_final: 0.7012 (m-10) REVERT: C 411 HIS cc_start: 0.8884 (t70) cc_final: 0.8660 (t70) REVERT: C 443 LEU cc_start: 0.8553 (mt) cc_final: 0.8268 (tt) REVERT: D 20 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9080 (mp) REVERT: D 141 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7634 (p0) REVERT: D 180 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8803 (pp) REVERT: D 311 GLN cc_start: 0.6313 (pm20) cc_final: 0.6093 (pm20) REVERT: E 311 GLN cc_start: 0.6450 (pm20) cc_final: 0.6176 (pm20) REVERT: E 322 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8293 (tpp80) outliers start: 69 outliers final: 48 residues processed: 221 average time/residue: 0.2729 time to fit residues: 92.8798 Evaluate side-chains 200 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 147 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 188 optimal weight: 0.0970 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17350 Z= 0.201 Angle : 0.633 10.684 23715 Z= 0.297 Chirality : 0.048 0.389 2820 Planarity : 0.004 0.032 2855 Dihedral : 7.062 55.937 2950 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.16 % Allowed : 16.08 % Favored : 80.76 % 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 (0.19), residues: 1950 helix: 1.23 (0.20), residues: 740 sheet: -1.82 (0.21), residues: 475 loop : -2.03 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 320 HIS 0.013 0.001 HIS A 411 PHE 0.016 0.001 PHE A 233 TYR 0.013 0.001 TYR D 67 ARG 0.015 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 175 time to evaluate : 2.471 Fit side-chains REVERT: A 268 ILE cc_start: 0.8946 (tp) cc_final: 0.8741 (tt) REVERT: A 320 TRP cc_start: 0.7223 (m-10) cc_final: 0.6961 (m-10) REVERT: A 417 ASP cc_start: 0.8362 (p0) cc_final: 0.8035 (p0) REVERT: B 103 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8683 (m-10) REVERT: C 180 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8666 (pp) REVERT: C 320 TRP cc_start: 0.7177 (m-10) cc_final: 0.6896 (m-10) REVERT: C 411 HIS cc_start: 0.8870 (t70) cc_final: 0.8659 (t70) REVERT: C 443 LEU cc_start: 0.8568 (mt) cc_final: 0.8282 (tt) REVERT: D 20 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9057 (mp) REVERT: D 141 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7548 (p0) REVERT: D 180 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (pp) REVERT: D 320 TRP cc_start: 0.8114 (m-90) cc_final: 0.7881 (m-90) REVERT: E 139 ILE cc_start: 0.8921 (mm) cc_final: 0.8458 (pt) REVERT: E 311 GLN cc_start: 0.6455 (pm20) cc_final: 0.6226 (pm20) REVERT: E 322 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8290 (tpp80) outliers start: 58 outliers final: 43 residues processed: 222 average time/residue: 0.2779 time to fit residues: 94.2088 Evaluate side-chains 206 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 187 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17350 Z= 0.232 Angle : 0.646 10.863 23715 Z= 0.305 Chirality : 0.048 0.387 2820 Planarity : 0.004 0.054 2855 Dihedral : 6.872 56.289 2950 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.54 % Allowed : 16.57 % Favored : 79.89 % 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: -0.91 (0.19), residues: 1950 helix: 1.51 (0.20), residues: 740 sheet: -1.79 (0.21), residues: 480 loop : -1.95 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 456 HIS 0.002 0.000 HIS C 460 PHE 0.020 0.001 PHE A 233 TYR 0.013 0.001 TYR C 67 ARG 0.010 0.001 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 159 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 320 TRP cc_start: 0.7202 (m-10) cc_final: 0.6888 (m-10) REVERT: B 103 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8709 (m-10) REVERT: C 180 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8693 (pp) REVERT: C 320 TRP cc_start: 0.7154 (m-10) cc_final: 0.6859 (m-10) REVERT: C 411 HIS cc_start: 0.8864 (t70) cc_final: 0.8643 (t70) REVERT: C 443 LEU cc_start: 0.8567 (mt) cc_final: 0.8285 (tt) REVERT: D 20 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9061 (mp) REVERT: D 141 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7569 (p0) REVERT: D 180 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8764 (pp) REVERT: E 139 ILE cc_start: 0.8944 (mm) cc_final: 0.8512 (pt) REVERT: E 311 GLN cc_start: 0.6534 (pm20) cc_final: 0.6324 (pm20) outliers start: 65 outliers final: 49 residues processed: 208 average time/residue: 0.2739 time to fit residues: 87.7076 Evaluate side-chains 206 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17350 Z= 0.200 Angle : 0.637 10.664 23715 Z= 0.300 Chirality : 0.048 0.384 2820 Planarity : 0.004 0.061 2855 Dihedral : 6.635 55.968 2950 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.43 % Allowed : 17.06 % Favored : 79.51 % 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: -0.69 (0.19), residues: 1950 helix: 1.77 (0.20), residues: 740 sheet: -1.72 (0.21), residues: 475 loop : -1.88 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 456 HIS 0.002 0.000 HIS C 460 PHE 0.018 0.001 PHE A 233 TYR 0.013 0.001 TYR D 67 ARG 0.009 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 1.971 Fit side-chains revert: symmetry clash REVERT: A 320 TRP cc_start: 0.7125 (m-10) cc_final: 0.6850 (m-10) REVERT: B 103 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8688 (m-10) REVERT: C 180 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 320 TRP cc_start: 0.7128 (m-10) cc_final: 0.6832 (m-10) REVERT: C 411 HIS cc_start: 0.8895 (t70) cc_final: 0.8655 (t70) REVERT: C 443 LEU cc_start: 0.8563 (mt) cc_final: 0.8282 (tt) REVERT: D 20 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9056 (mp) REVERT: D 141 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7538 (p0) REVERT: D 180 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 139 ILE cc_start: 0.8947 (mm) cc_final: 0.8546 (pt) outliers start: 63 outliers final: 48 residues processed: 208 average time/residue: 0.2722 time to fit residues: 87.0974 Evaluate side-chains 199 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 146 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 175 optimal weight: 0.0470 chunk 105 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17350 Z= 0.157 Angle : 0.615 9.832 23715 Z= 0.288 Chirality : 0.047 0.378 2820 Planarity : 0.004 0.045 2855 Dihedral : 6.199 54.933 2950 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.56 % Allowed : 17.93 % Favored : 79.51 % 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: -0.50 (0.20), residues: 1950 helix: 1.97 (0.20), residues: 740 sheet: -1.66 (0.21), residues: 475 loop : -1.81 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 456 HIS 0.002 0.000 HIS E 309 PHE 0.017 0.001 PHE A 233 TYR 0.012 0.001 TYR D 67 ARG 0.010 0.000 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: B 103 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: C 139 ILE cc_start: 0.8969 (mm) cc_final: 0.8494 (pt) REVERT: C 180 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8685 (pp) REVERT: C 411 HIS cc_start: 0.8896 (t70) cc_final: 0.8645 (t70) REVERT: C 443 LEU cc_start: 0.8542 (mt) cc_final: 0.8265 (tt) REVERT: D 20 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9084 (mp) REVERT: D 180 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8730 (pp) REVERT: E 139 ILE cc_start: 0.8934 (mm) cc_final: 0.8530 (pt) outliers start: 47 outliers final: 36 residues processed: 205 average time/residue: 0.2673 time to fit residues: 84.2226 Evaluate side-chains 196 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 154 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 94 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17350 Z= 0.199 Angle : 0.641 10.282 23715 Z= 0.298 Chirality : 0.047 0.381 2820 Planarity : 0.004 0.052 2855 Dihedral : 6.175 55.738 2950 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.40 % Allowed : 18.09 % Favored : 79.51 % 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: -0.39 (0.20), residues: 1950 helix: 2.08 (0.20), residues: 740 sheet: -1.59 (0.21), residues: 475 loop : -1.76 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 320 HIS 0.002 0.000 HIS E 309 PHE 0.019 0.001 PHE A 233 TYR 0.015 0.001 TYR D 448 ARG 0.009 0.001 ARG D 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 180 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8707 (pp) REVERT: C 411 HIS cc_start: 0.8904 (t70) cc_final: 0.8644 (t70) REVERT: C 443 LEU cc_start: 0.8536 (mt) cc_final: 0.8257 (tt) REVERT: D 20 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9083 (mp) REVERT: D 180 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8730 (pp) REVERT: E 139 ILE cc_start: 0.8949 (mm) cc_final: 0.8549 (pt) outliers start: 44 outliers final: 38 residues processed: 186 average time/residue: 0.2812 time to fit residues: 80.3926 Evaluate side-chains 191 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.069559 restraints weight = 29589.797| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.91 r_work: 0.2678 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17350 Z= 0.177 Angle : 0.635 10.025 23715 Z= 0.296 Chirality : 0.047 0.378 2820 Planarity : 0.004 0.047 2855 Dihedral : 6.075 55.205 2950 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.29 % Allowed : 18.37 % Favored : 79.35 % 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: -0.30 (0.20), residues: 1950 helix: 2.16 (0.20), residues: 740 sheet: -1.57 (0.21), residues: 475 loop : -1.72 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 456 HIS 0.001 0.000 HIS A 460 PHE 0.024 0.001 PHE A 233 TYR 0.014 0.001 TYR D 448 ARG 0.009 0.000 ARG C 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3400.58 seconds wall clock time: 62 minutes 26.23 seconds (3746.23 seconds total)