Starting phenix.real_space_refine on Wed Mar 20 09:56:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bej_16005/03_2024/8bej_16005_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bej_16005/03_2024/8bej_16005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bej_16005/03_2024/8bej_16005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bej_16005/03_2024/8bej_16005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bej_16005/03_2024/8bej_16005_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bej_16005/03_2024/8bej_16005_trim.pdb" } resolution = 3.24 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8835 2.51 5 N 2260 2.21 5 O 2470 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27065 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.00, per 1000 atoms: 0.41 Number of scatterers: 27065 At special positions: 0 Unit cell: (93.888, 91.28, 123.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2470 8.00 N 2260 7.00 C 8835 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 20.71 Conformation dependent library (CDL) restraints added in 2.7 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 42.3% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.572A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 97 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 4.017A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.572A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 90 through 97 removed outlier: 3.531A pdb=" N LEU B 93 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B 95 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.572A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU C 93 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.519A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.571A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU D 93 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 97 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.571A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU E 93 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE E 97 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 4.415A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 137 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 62 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 56 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 64 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 68 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 50 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA A 70 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET A 48 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A 72 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR A 46 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LYS A 74 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 44 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 6.622A pdb=" N GLU A 62 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 56 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 64 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 68 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 50 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA A 70 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET A 48 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A 72 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR A 46 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LYS A 74 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 44 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 4.414A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 137 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B 62 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL B 56 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 68 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 50 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 70 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET B 48 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR B 72 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR B 46 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS B 74 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 44 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 6.622A pdb=" N GLU B 62 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL B 56 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 68 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 50 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 70 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET B 48 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR B 72 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR B 46 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS B 74 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 44 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 4.415A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 137 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 62 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 56 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 64 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 68 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL C 50 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA C 70 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET C 48 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 72 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR C 46 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS C 74 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL C 44 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.623A pdb=" N GLU C 62 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 56 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 64 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 68 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL C 50 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA C 70 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET C 48 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 72 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR C 46 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS C 74 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL C 44 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.499A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 4.415A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 137 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU D 62 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 56 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 64 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 68 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 50 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA D 70 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET D 48 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR D 72 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR D 46 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS D 74 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 44 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.622A pdb=" N GLU D 62 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 56 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 64 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 68 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 50 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA D 70 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET D 48 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR D 72 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR D 46 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS D 74 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 44 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 4.414A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 137 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU E 62 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL E 56 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE E 68 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 50 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA E 70 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET E 48 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR E 72 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR E 46 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS E 74 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 44 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 6.621A pdb=" N GLU E 62 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL E 56 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE E 68 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 50 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA E 70 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET E 48 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR E 72 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR E 46 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS E 74 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 44 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2280 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: 10.38 Time building geometry restraints manager: 21.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 0 1.23 - 1.42: 6035 1.42 - 1.61: 7825 1.61 - 1.81: 150 Bond restraints: 27425 Sorted by residual: bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27420 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.34: 647 107.34 - 114.00: 32120 114.00 - 120.67: 9559 120.67 - 127.33: 6831 127.33 - 134.00: 178 Bond angle restraints: 49335 Sorted by residual: angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 1.00e+01 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 9.99e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.79e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.78e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.77e+00 ... (remaining 49330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.29: 12145 12.29 - 24.57: 690 24.57 - 36.86: 100 36.86 - 49.15: 80 49.15 - 61.44: 85 Dihedral angle restraints: 13100 sinusoidal: 6970 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " pdb=" CD LYS A 315 " pdb=" CE LYS A 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.27 -40.27 3 1.50e+01 4.44e-03 7.17e+00 dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.26 -40.26 3 1.50e+01 4.44e-03 7.17e+00 dihedral pdb=" CB LYS E 315 " pdb=" CG LYS E 315 " pdb=" CD LYS E 315 " pdb=" CE LYS E 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.25 -40.25 3 1.50e+01 4.44e-03 7.17e+00 ... (remaining 13097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1325 0.024 - 0.048: 519 0.048 - 0.071: 144 0.071 - 0.095: 78 0.095 - 0.119: 94 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 205 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 2157 not shown) Planarity restraints: 3980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 149 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.35e-01 pdb=" N PRO B 150 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 149 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.31e-01 pdb=" N PRO C 150 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 150 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 150 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 149 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.29e-01 pdb=" N PRO E 150 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO E 150 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 150 " -0.012 5.00e-02 4.00e+02 ... (remaining 3977 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 4682 2.29 - 2.87: 62535 2.87 - 3.45: 68581 3.45 - 4.02: 96053 4.02 - 4.60: 146626 Nonbonded interactions: 378477 Sorted by model distance: nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.718 1.850 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.718 1.850 nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.718 1.850 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.718 1.850 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.719 1.850 ... (remaining 378472 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' } 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: 7.930 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: 0.380 Extract box with map and model: 29.770 Check model and map are aligned: 0.450 Set scattering table: 0.240 Process input model: 83.100 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14010 Z= 0.127 Angle : 0.373 5.693 19060 Z= 0.187 Chirality : 0.037 0.119 2160 Planarity : 0.003 0.023 2375 Dihedral : 6.958 61.435 5090 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.70 (0.22), residues: 1670 helix: 2.94 (0.22), residues: 575 sheet: -0.22 (0.25), residues: 485 loop : 0.67 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 73 HIS 0.002 0.001 HIS C 195 PHE 0.003 0.001 PHE E 69 TYR 0.005 0.001 TYR B 285 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 GLN cc_start: 0.8052 (mm110) cc_final: 0.7777 (mm110) REVERT: D 232 GLN cc_start: 0.9321 (tp40) cc_final: 0.9109 (tp40) REVERT: E 85 GLN cc_start: 0.8069 (mm110) cc_final: 0.7843 (mm110) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.6723 time to fit residues: 173.7817 Evaluate side-chains 124 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14010 Z= 0.478 Angle : 0.619 5.855 19060 Z= 0.337 Chirality : 0.044 0.147 2160 Planarity : 0.005 0.043 2375 Dihedral : 3.989 20.927 1955 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.40 % Allowed : 5.10 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1670 helix: 2.27 (0.21), residues: 615 sheet: -0.19 (0.26), residues: 420 loop : -0.00 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 114 HIS 0.003 0.001 HIS E 105 PHE 0.019 0.002 PHE E 53 TYR 0.011 0.002 TYR B 297 ARG 0.004 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8268 (mm110) cc_final: 0.7933 (mm110) REVERT: A 114 TRP cc_start: 0.7549 (m100) cc_final: 0.7240 (m100) REVERT: B 85 GLN cc_start: 0.8321 (mm110) cc_final: 0.7989 (mm110) REVERT: B 114 TRP cc_start: 0.7667 (m100) cc_final: 0.7360 (m100) REVERT: C 114 TRP cc_start: 0.7600 (m100) cc_final: 0.7279 (m100) REVERT: D 85 GLN cc_start: 0.8296 (mm110) cc_final: 0.7963 (mm110) REVERT: D 114 TRP cc_start: 0.7551 (m100) cc_final: 0.7198 (m100) outliers start: 6 outliers final: 5 residues processed: 142 average time/residue: 0.5567 time to fit residues: 117.3432 Evaluate side-chains 122 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN C 410 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN E 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14010 Z= 0.194 Angle : 0.451 4.551 19060 Z= 0.240 Chirality : 0.040 0.144 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.500 11.563 1955 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.55 (0.21), residues: 1670 helix: 2.84 (0.21), residues: 615 sheet: 0.19 (0.28), residues: 385 loop : -0.14 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.003 0.001 HIS A 105 PHE 0.009 0.001 PHE D 301 TYR 0.013 0.001 TYR B 297 ARG 0.003 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7513 (m100) cc_final: 0.7177 (m100) REVERT: B 85 GLN cc_start: 0.8311 (mm110) cc_final: 0.8005 (mm110) REVERT: B 114 TRP cc_start: 0.7593 (m100) cc_final: 0.7190 (m100) REVERT: C 114 TRP cc_start: 0.7554 (m100) cc_final: 0.7167 (m100) REVERT: D 85 GLN cc_start: 0.8257 (mm110) cc_final: 0.7938 (mm110) REVERT: D 114 TRP cc_start: 0.7480 (m100) cc_final: 0.7111 (m100) REVERT: D 245 GLN cc_start: 0.8557 (mp10) cc_final: 0.8276 (tm-30) REVERT: E 114 TRP cc_start: 0.7583 (m100) cc_final: 0.7197 (m100) REVERT: E 216 MET cc_start: 0.8880 (mmm) cc_final: 0.8370 (mmm) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.5623 time to fit residues: 107.6024 Evaluate side-chains 119 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 14010 Z= 0.293 Angle : 0.475 4.627 19060 Z= 0.255 Chirality : 0.040 0.141 2160 Planarity : 0.004 0.065 2375 Dihedral : 3.678 15.093 1955 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.38 (0.21), residues: 1670 helix: 2.87 (0.21), residues: 615 sheet: -0.08 (0.27), residues: 395 loop : -0.30 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 414 HIS 0.002 0.001 HIS B 105 PHE 0.010 0.001 PHE B 409 TYR 0.017 0.001 TYR B 297 ARG 0.011 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8239 (mm110) cc_final: 0.7908 (mm110) REVERT: A 114 TRP cc_start: 0.7560 (m100) cc_final: 0.7209 (m100) REVERT: A 245 GLN cc_start: 0.8636 (mp10) cc_final: 0.8346 (tm-30) REVERT: B 114 TRP cc_start: 0.7617 (m100) cc_final: 0.7224 (m100) REVERT: C 114 TRP cc_start: 0.7575 (m100) cc_final: 0.7168 (m100) REVERT: D 85 GLN cc_start: 0.8293 (mm110) cc_final: 0.7953 (mm110) REVERT: D 114 TRP cc_start: 0.7524 (m100) cc_final: 0.7115 (m100) REVERT: D 245 GLN cc_start: 0.8586 (mp10) cc_final: 0.8317 (tm-30) REVERT: E 114 TRP cc_start: 0.7633 (m100) cc_final: 0.7240 (m100) REVERT: E 306 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8857 (tm-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.5317 time to fit residues: 91.0717 Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14010 Z= 0.232 Angle : 0.444 4.439 19060 Z= 0.237 Chirality : 0.040 0.145 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.552 12.791 1955 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.20 % Allowed : 7.45 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.47 (0.21), residues: 1670 helix: 3.13 (0.20), residues: 610 sheet: -0.06 (0.27), residues: 390 loop : -0.41 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS B 105 PHE 0.031 0.001 PHE A 301 TYR 0.011 0.001 TYR B 297 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8258 (mm110) cc_final: 0.7929 (mm110) REVERT: A 114 TRP cc_start: 0.7540 (m100) cc_final: 0.7190 (m100) REVERT: A 245 GLN cc_start: 0.8635 (mp10) cc_final: 0.8282 (tm-30) REVERT: B 114 TRP cc_start: 0.7601 (m100) cc_final: 0.7191 (m100) REVERT: C 114 TRP cc_start: 0.7571 (m100) cc_final: 0.7160 (m100) REVERT: D 114 TRP cc_start: 0.7511 (m100) cc_final: 0.7103 (m100) REVERT: D 245 GLN cc_start: 0.8593 (mp10) cc_final: 0.8304 (tm-30) REVERT: E 114 TRP cc_start: 0.7633 (m100) cc_final: 0.7232 (m100) REVERT: E 306 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8843 (tm-30) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.5777 time to fit residues: 100.0030 Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 14010 Z= 0.416 Angle : 0.525 4.755 19060 Z= 0.286 Chirality : 0.041 0.140 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.987 20.256 1955 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.13 % Allowed : 8.32 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.96 (0.20), residues: 1670 helix: 2.74 (0.20), residues: 615 sheet: -0.61 (0.24), residues: 440 loop : -0.53 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 73 HIS 0.003 0.001 HIS B 105 PHE 0.011 0.002 PHE A 301 TYR 0.018 0.001 TYR B 297 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7559 (m100) cc_final: 0.7183 (m100) REVERT: B 114 TRP cc_start: 0.7657 (m100) cc_final: 0.7230 (m100) REVERT: C 114 TRP cc_start: 0.7622 (m100) cc_final: 0.7221 (m100) REVERT: D 114 TRP cc_start: 0.7572 (m100) cc_final: 0.7166 (m100) REVERT: E 114 TRP cc_start: 0.7669 (m100) cc_final: 0.7255 (m100) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.6005 time to fit residues: 99.3411 Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14010 Z= 0.189 Angle : 0.437 4.811 19060 Z= 0.231 Chirality : 0.040 0.181 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.582 12.759 1955 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 7.99 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.40 (0.21), residues: 1670 helix: 3.21 (0.20), residues: 610 sheet: -0.25 (0.27), residues: 390 loop : -0.51 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS B 105 PHE 0.016 0.001 PHE A 301 TYR 0.012 0.001 TYR B 297 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7537 (m100) cc_final: 0.7155 (m100) REVERT: A 216 MET cc_start: 0.8780 (mmm) cc_final: 0.8529 (mmm) REVERT: A 245 GLN cc_start: 0.8633 (mp10) cc_final: 0.8306 (tm-30) REVERT: B 114 TRP cc_start: 0.7602 (m100) cc_final: 0.7180 (m100) REVERT: C 114 TRP cc_start: 0.7577 (m100) cc_final: 0.7194 (m100) REVERT: C 232 GLN cc_start: 0.9368 (tp40) cc_final: 0.9141 (tp40) REVERT: D 114 TRP cc_start: 0.7558 (m100) cc_final: 0.7168 (m100) REVERT: D 216 MET cc_start: 0.8837 (mmm) cc_final: 0.8271 (mmm) REVERT: D 245 GLN cc_start: 0.8595 (mp10) cc_final: 0.8300 (tm-30) REVERT: E 114 TRP cc_start: 0.7610 (m100) cc_final: 0.7200 (m100) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.5752 time to fit residues: 98.2675 Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 14010 Z= 0.301 Angle : 0.473 4.629 19060 Z= 0.254 Chirality : 0.040 0.167 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.734 15.578 1955 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.07 % Allowed : 8.46 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.21 (0.21), residues: 1670 helix: 3.10 (0.20), residues: 610 sheet: -0.47 (0.25), residues: 415 loop : -0.56 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 73 HIS 0.003 0.001 HIS B 105 PHE 0.012 0.001 PHE A 301 TYR 0.011 0.001 TYR B 297 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7559 (m100) cc_final: 0.7188 (m100) REVERT: A 216 MET cc_start: 0.8798 (mmm) cc_final: 0.8521 (mmm) REVERT: A 245 GLN cc_start: 0.8653 (mp10) cc_final: 0.8311 (tm-30) REVERT: B 114 TRP cc_start: 0.7641 (m100) cc_final: 0.7225 (m100) REVERT: C 114 TRP cc_start: 0.7637 (m100) cc_final: 0.7232 (m100) REVERT: C 232 GLN cc_start: 0.9378 (tp40) cc_final: 0.9154 (tp40) REVERT: D 114 TRP cc_start: 0.7587 (m100) cc_final: 0.7190 (m100) REVERT: D 216 MET cc_start: 0.8843 (mmm) cc_final: 0.8231 (mmm) REVERT: D 245 GLN cc_start: 0.8606 (mp10) cc_final: 0.8314 (tm-30) REVERT: E 114 TRP cc_start: 0.7657 (m100) cc_final: 0.7248 (m100) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.6030 time to fit residues: 103.3781 Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14010 Z= 0.146 Angle : 0.426 5.123 19060 Z= 0.224 Chirality : 0.040 0.181 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.471 13.107 1955 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.07 % Allowed : 8.59 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.56 (0.21), residues: 1670 helix: 3.39 (0.20), residues: 610 sheet: -0.15 (0.27), residues: 390 loop : -0.46 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS C 105 PHE 0.014 0.001 PHE A 301 TYR 0.010 0.001 TYR C 297 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7555 (m100) cc_final: 0.7171 (m100) REVERT: A 216 MET cc_start: 0.8768 (mmm) cc_final: 0.8487 (mmm) REVERT: A 245 GLN cc_start: 0.8685 (mp10) cc_final: 0.8249 (tm-30) REVERT: B 114 TRP cc_start: 0.7616 (m100) cc_final: 0.7209 (m100) REVERT: B 216 MET cc_start: 0.8928 (mmm) cc_final: 0.8312 (mmm) REVERT: B 245 GLN cc_start: 0.8767 (mp10) cc_final: 0.8340 (tm-30) REVERT: C 114 TRP cc_start: 0.7581 (m100) cc_final: 0.7185 (m100) REVERT: C 232 GLN cc_start: 0.9358 (tp40) cc_final: 0.9137 (tp40) REVERT: D 114 TRP cc_start: 0.7552 (m100) cc_final: 0.7155 (m100) REVERT: D 216 MET cc_start: 0.8821 (mmm) cc_final: 0.8227 (mmm) REVERT: D 245 GLN cc_start: 0.8606 (mp10) cc_final: 0.8316 (tm-30) REVERT: E 114 TRP cc_start: 0.7605 (m100) cc_final: 0.7196 (m100) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.5854 time to fit residues: 106.5585 Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14010 Z= 0.245 Angle : 0.455 4.708 19060 Z= 0.242 Chirality : 0.040 0.168 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.564 13.023 1955 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.07 % Allowed : 8.93 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.45 (0.21), residues: 1670 helix: 3.25 (0.20), residues: 610 sheet: -0.16 (0.27), residues: 390 loop : -0.51 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 73 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.001 PHE A 301 TYR 0.016 0.001 TYR D 297 ARG 0.003 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7581 (m100) cc_final: 0.7189 (m100) REVERT: A 239 MET cc_start: 0.8934 (mmm) cc_final: 0.8631 (mmt) REVERT: A 245 GLN cc_start: 0.8680 (mp10) cc_final: 0.8325 (tm-30) REVERT: B 114 TRP cc_start: 0.7632 (m100) cc_final: 0.7214 (m100) REVERT: B 216 MET cc_start: 0.8942 (mmm) cc_final: 0.8348 (mmm) REVERT: C 114 TRP cc_start: 0.7614 (m100) cc_final: 0.7212 (m100) REVERT: C 232 GLN cc_start: 0.9358 (tp40) cc_final: 0.9141 (tp40) REVERT: D 114 TRP cc_start: 0.7585 (m100) cc_final: 0.7184 (m100) REVERT: D 245 GLN cc_start: 0.8619 (mp10) cc_final: 0.8299 (tm-30) REVERT: E 114 TRP cc_start: 0.7654 (m100) cc_final: 0.7235 (m100) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.5505 time to fit residues: 92.5584 Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.066060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055973 restraints weight = 128505.932| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.58 r_work: 0.2983 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14010 Z= 0.282 Angle : 0.472 4.613 19060 Z= 0.253 Chirality : 0.040 0.166 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.694 13.734 1955 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.07 % Allowed : 9.13 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.34 (0.21), residues: 1670 helix: 3.15 (0.20), residues: 610 sheet: -0.32 (0.26), residues: 410 loop : -0.49 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 73 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.001 PHE B 301 TYR 0.016 0.001 TYR D 297 ARG 0.003 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4932.83 seconds wall clock time: 88 minutes 50.66 seconds (5330.66 seconds total)