Starting phenix.real_space_refine on Sun Jul 21 08:26:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp3_41465/07_2024/8tp3_41465.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp3_41465/07_2024/8tp3_41465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp3_41465/07_2024/8tp3_41465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp3_41465/07_2024/8tp3_41465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp3_41465/07_2024/8tp3_41465.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp3_41465/07_2024/8tp3_41465.cif" } resolution = 3.6 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= 0.026 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 59 5.16 5 C 8613 2.51 5 N 2322 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 278": "OD1" <-> "OD2" Residue "G PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13691 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1377 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1377 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.43, per 1000 atoms: 0.54 Number of scatterers: 13691 At special positions: 0 Unit cell: (98.9, 96.6, 179.4, 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 59 16.00 O 2697 8.00 N 2322 7.00 C 8613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.06 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.06 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.02 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.04 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.02 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 63 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 63 " " NAG C 404 " - " ASN C 129 " " NAG C 405 " - " ASN C 163 " " NAG E 1 " - " ASN A 95 " " NAG F 1 " - " ASN C 95 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 33 " " NAG G 403 " - " ASN G 63 " " NAG G 404 " - " ASN G 129 " " NAG J 1 " - " ASN G 95 " Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 2.2 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 38 sheets defined 25.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.896A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.216A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.929A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.221A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.991A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 114 removed outlier: 4.104A pdb=" N SER G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 removed outlier: 4.697A pdb=" N TRP G 127 " --> pdb=" O LYS G 125A" (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.339A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.471A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.587A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.587A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.661A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.991A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.332A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.162A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.162A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 144 through 146 removed outlier: 4.719A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.908A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 31 through 36 Processing sheet with id=AC5, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.353A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS G 277 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 62 removed outlier: 6.162A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 115 through 122 removed outlier: 7.218A pdb=" N SER G 261 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 118 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA G 259 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G 120 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 257 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 115 through 122 removed outlier: 7.218A pdb=" N SER G 261 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 118 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA G 259 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G 120 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 257 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.266A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'G' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.493A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.493A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.948A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.948A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1650 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: 4.76 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3995 1.33 - 1.47: 4264 1.47 - 1.61: 5680 1.61 - 1.75: 8 1.75 - 1.89: 73 Bond restraints: 14020 Sorted by residual: bond pdb=" CB HIS H 52 " pdb=" CG HIS H 52 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.79e+01 bond pdb=" CB HIS G 47 " pdb=" CG HIS G 47 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.13e+01 bond pdb=" N CYS D 137 " pdb=" CA CYS D 137 " ideal model delta sigma weight residual 1.458 1.522 -0.065 1.19e-02 7.06e+03 2.95e+01 bond pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" CG PHE D 9 " pdb=" CD1 PHE D 9 " ideal model delta sigma weight residual 1.384 1.493 -0.109 2.10e-02 2.27e+03 2.67e+01 ... (remaining 14015 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.63: 253 104.63 - 112.10: 6320 112.10 - 119.57: 5740 119.57 - 127.04: 6536 127.04 - 134.51: 183 Bond angle restraints: 19032 Sorted by residual: angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.54 -6.88 7.30e-01 1.88e+00 8.88e+01 angle pdb=" C HIS G 184 " pdb=" N PRO G 185 " pdb=" CA PRO G 185 " ideal model delta sigma weight residual 119.66 126.33 -6.67 7.30e-01 1.88e+00 8.35e+01 angle pdb=" C ILE A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 120.31 127.58 -7.27 9.80e-01 1.04e+00 5.50e+01 angle pdb=" N LYS A 32 " pdb=" CA LYS A 32 " pdb=" C LYS A 32 " ideal model delta sigma weight residual 111.82 120.16 -8.34 1.16e+00 7.43e-01 5.17e+01 angle pdb=" C CYS C 305 " pdb=" N PRO C 306 " pdb=" CA PRO C 306 " ideal model delta sigma weight residual 119.78 127.11 -7.33 1.03e+00 9.43e-01 5.07e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 8348 21.02 - 42.05: 168 42.05 - 63.07: 51 63.07 - 84.09: 16 84.09 - 105.12: 7 Dihedral angle restraints: 8590 sinusoidal: 3687 harmonic: 4903 Sorted by residual: dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual -86.00 -9.50 -76.50 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 148.33 -55.33 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -45.01 -40.99 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1526 0.104 - 0.208: 454 0.208 - 0.312: 71 0.312 - 0.416: 30 0.416 - 0.520: 14 Chirality restraints: 2095 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.29e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.67e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.24e+01 ... (remaining 2092 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.122 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C7 NAG A 401 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.159 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 401 " 0.096 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG G 401 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG G 401 " -0.025 2.00e-02 2.50e+03 pdb=" N2 NAG G 401 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG G 401 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 95 " 0.075 2.00e-02 2.50e+03 7.74e-02 7.49e+01 pdb=" CG ASN C 95 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 95 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 95 " -0.119 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.093 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4616 2.85 - 3.36: 12475 3.36 - 3.87: 24009 3.87 - 4.39: 28160 4.39 - 4.90: 45794 Nonbonded interactions: 115054 Sorted by model distance: nonbonded pdb=" NZ LYS D 83 " pdb=" OD1 ASP I 85 " model vdw 2.336 2.520 nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP D 85 " model vdw 2.342 2.520 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS I 83 " model vdw 2.350 2.520 nonbonded pdb=" N ASP B 19 " pdb=" OD1 ASP B 19 " model vdw 2.380 2.520 nonbonded pdb=" N ASN H 76 " pdb=" N GLN H 77 " model vdw 2.396 2.560 ... (remaining 115049 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 'C' and (resid 11 through 325 or resid 401 through 404)) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 9 through 171) selection = chain 'D' selection = (chain 'I' and resid 9 through 171) } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.990 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.020 0.121 14020 Z= 1.299 Angle : 1.720 13.305 19032 Z= 1.150 Chirality : 0.110 0.520 2095 Planarity : 0.009 0.122 2451 Dihedral : 10.547 105.117 5402 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.78 (0.19), residues: 1684 helix: 0.86 (0.24), residues: 358 sheet: 0.89 (0.26), residues: 330 loop : 0.38 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.007 TRP D 21 HIS 0.010 0.003 HIS C 38 PHE 0.052 0.007 PHE H 100J TYR 0.050 0.009 TYR D 157 ARG 0.009 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 1.654 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: A 82 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6593 (mmmt) REVERT: A 104 ASP cc_start: 0.9064 (m-30) cc_final: 0.8862 (m-30) REVERT: A 274 MET cc_start: 0.7445 (mtt) cc_final: 0.7236 (ttt) REVERT: B 46 ASN cc_start: 0.7856 (m-40) cc_final: 0.7608 (t0) REVERT: B 53 ASN cc_start: 0.6760 (m-40) cc_final: 0.5744 (t0) REVERT: C 82 LYS cc_start: 0.7522 (mmtt) cc_final: 0.6903 (tptp) REVERT: D 11 GLU cc_start: 0.7209 (tt0) cc_final: 0.6938 (pm20) REVERT: D 77 MET cc_start: 0.7521 (ttt) cc_final: 0.7133 (ttm) REVERT: D 142 HIS cc_start: 0.8256 (p90) cc_final: 0.7765 (p90) REVERT: G 75 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6818 (mm-30) REVERT: G 107 GLU cc_start: 0.8307 (tp30) cc_final: 0.8094 (tp30) REVERT: G 148 TYR cc_start: 0.8047 (m-80) cc_final: 0.7523 (m-80) REVERT: G 201 TYR cc_start: 0.7945 (p90) cc_final: 0.7215 (p90) REVERT: G 224 ARG cc_start: 0.8435 (mtp85) cc_final: 0.6353 (mpt180) REVERT: G 256 TYR cc_start: 0.8342 (m-80) cc_final: 0.7913 (m-10) REVERT: I 34 TYR cc_start: 0.5419 (m-80) cc_final: 0.5105 (m-80) REVERT: I 109 ASP cc_start: 0.8289 (m-30) cc_final: 0.7822 (t70) REVERT: H 3 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7479 (mm110) REVERT: H 36 TRP cc_start: 0.7984 (m100) cc_final: 0.7323 (m100) REVERT: H 100 PHE cc_start: 0.7508 (m-80) cc_final: 0.7218 (m-80) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.2794 time to fit residues: 191.6808 Evaluate side-chains 238 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN C 282 GLN C 295 GLN C 298 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 14020 Z= 0.287 Angle : 0.702 8.351 19032 Z= 0.379 Chirality : 0.048 0.440 2095 Planarity : 0.005 0.055 2451 Dihedral : 6.994 66.705 2253 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.85 % Allowed : 10.28 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.82 (0.19), residues: 1684 helix: 1.89 (0.26), residues: 361 sheet: 0.93 (0.31), residues: 267 loop : 0.01 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 153 HIS 0.010 0.002 HIS A 196 PHE 0.021 0.003 PHE G 118 TYR 0.019 0.002 TYR B 157 ARG 0.007 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 274 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8100 (mmmt) REVERT: A 104 ASP cc_start: 0.9110 (m-30) cc_final: 0.8894 (m-30) REVERT: A 274 MET cc_start: 0.7408 (mtt) cc_final: 0.7167 (ttt) REVERT: B 17 MET cc_start: 0.7276 (ttt) cc_final: 0.6988 (ttt) REVERT: B 53 ASN cc_start: 0.6598 (m-40) cc_final: 0.5775 (t0) REVERT: B 120 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7846 (tt0) REVERT: B 128 ASN cc_start: 0.8071 (m110) cc_final: 0.7409 (t0) REVERT: B 141 TYR cc_start: 0.6237 (m-80) cc_final: 0.5161 (m-80) REVERT: C 82 LYS cc_start: 0.7628 (mmtt) cc_final: 0.6965 (tptp) REVERT: C 226 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7678 (mm-40) REVERT: C 295 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: D 77 MET cc_start: 0.7239 (ttt) cc_final: 0.7025 (ttm) REVERT: D 142 HIS cc_start: 0.8378 (p90) cc_final: 0.7721 (p90) REVERT: G 107 GLU cc_start: 0.8175 (tp30) cc_final: 0.7822 (tp30) REVERT: G 148 TYR cc_start: 0.7976 (m-80) cc_final: 0.7445 (m-80) REVERT: G 224 ARG cc_start: 0.8435 (mtp85) cc_final: 0.6184 (mtt180) REVERT: I 59 MET cc_start: 0.5849 (tpp) cc_final: 0.5613 (tpp) REVERT: I 109 ASP cc_start: 0.8279 (m-30) cc_final: 0.7732 (t70) REVERT: H 36 TRP cc_start: 0.8352 (m100) cc_final: 0.7716 (m100) REVERT: L 1 GLU cc_start: 0.5559 (pp20) cc_final: 0.5211 (mp0) REVERT: L 89 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: L 100 GLN cc_start: 0.7920 (pm20) cc_final: 0.7639 (pm20) outliers start: 57 outliers final: 33 residues processed: 314 average time/residue: 0.2473 time to fit residues: 112.5944 Evaluate side-chains 261 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 226 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 chunk 122 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14020 Z= 0.220 Angle : 0.622 7.929 19032 Z= 0.327 Chirality : 0.047 0.404 2095 Planarity : 0.004 0.043 2451 Dihedral : 5.993 55.212 2253 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.45 % Allowed : 13.12 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.73 (0.19), residues: 1684 helix: 2.17 (0.26), residues: 361 sheet: 0.63 (0.31), residues: 272 loop : -0.12 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 96 HIS 0.006 0.001 HIS A 196 PHE 0.020 0.002 PHE H 78 TYR 0.016 0.002 TYR L 91 ARG 0.008 0.001 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8459 (t0) cc_final: 0.8208 (t0) REVERT: A 180 TRP cc_start: 0.8487 (p90) cc_final: 0.7746 (p90) REVERT: A 229 ARG cc_start: 0.8492 (mmt-90) cc_final: 0.8277 (mmt180) REVERT: A 274 MET cc_start: 0.7390 (mtt) cc_final: 0.7127 (ttt) REVERT: B 17 MET cc_start: 0.7256 (ttt) cc_final: 0.7052 (ttt) REVERT: B 53 ASN cc_start: 0.6567 (m-40) cc_final: 0.5788 (t0) REVERT: B 69 GLU cc_start: 0.5149 (tt0) cc_final: 0.4866 (tt0) REVERT: B 128 ASN cc_start: 0.8049 (m110) cc_final: 0.7729 (t0) REVERT: B 141 TYR cc_start: 0.6216 (m-80) cc_final: 0.5172 (m-80) REVERT: C 82 LYS cc_start: 0.7645 (mmtt) cc_final: 0.6975 (tptp) REVERT: C 83 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6840 (mm-30) REVERT: C 226 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7612 (mm-40) REVERT: D 58 LYS cc_start: 0.7368 (mmmt) cc_final: 0.7013 (mmtt) REVERT: D 77 MET cc_start: 0.7150 (ttt) cc_final: 0.6944 (ttm) REVERT: D 142 HIS cc_start: 0.7977 (p90) cc_final: 0.7573 (p90) REVERT: G 224 ARG cc_start: 0.8232 (mtp85) cc_final: 0.6003 (mtt180) REVERT: G 320 LEU cc_start: 0.8763 (mp) cc_final: 0.8501 (mt) REVERT: I 109 ASP cc_start: 0.8283 (m-30) cc_final: 0.7837 (t70) REVERT: H 3 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7446 (mm110) REVERT: L 11 LEU cc_start: 0.8026 (mt) cc_final: 0.7791 (tt) REVERT: L 89 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6674 (tt0) outliers start: 51 outliers final: 35 residues processed: 277 average time/residue: 0.2575 time to fit residues: 103.3981 Evaluate side-chains 251 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 141 HIS ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN G 208 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14020 Z= 0.245 Angle : 0.615 10.471 19032 Z= 0.320 Chirality : 0.046 0.402 2095 Planarity : 0.004 0.049 2451 Dihedral : 5.432 54.259 2253 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.80 % Allowed : 12.78 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.61 (0.20), residues: 1684 helix: 2.25 (0.27), residues: 363 sheet: 0.67 (0.32), residues: 251 loop : -0.30 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 96 HIS 0.005 0.001 HIS A 38 PHE 0.023 0.002 PHE H 78 TYR 0.029 0.002 TYR A 17 ARG 0.005 0.001 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 227 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8564 (t0) cc_final: 0.8296 (t0) REVERT: B 53 ASN cc_start: 0.6719 (m-40) cc_final: 0.5773 (t0) REVERT: B 125 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7198 (tt0) REVERT: B 141 TYR cc_start: 0.6393 (m-80) cc_final: 0.5215 (m-80) REVERT: C 225 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7637 (t70) REVERT: C 226 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7739 (mm-40) REVERT: D 45 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (mp) REVERT: D 58 LYS cc_start: 0.7364 (mmmt) cc_final: 0.7080 (mmtt) REVERT: D 77 MET cc_start: 0.7115 (ttt) cc_final: 0.6909 (ttm) REVERT: D 142 HIS cc_start: 0.8031 (p90) cc_final: 0.7720 (p90) REVERT: G 191 GLN cc_start: 0.8068 (tp40) cc_final: 0.7560 (tt0) REVERT: G 224 ARG cc_start: 0.8334 (mtp85) cc_final: 0.6114 (mtt180) REVERT: G 314 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5858 (mm) REVERT: G 320 LEU cc_start: 0.8713 (mp) cc_final: 0.8445 (mt) REVERT: I 109 ASP cc_start: 0.8410 (m-30) cc_final: 0.8074 (t70) REVERT: H 100 PHE cc_start: 0.7342 (m-80) cc_final: 0.6893 (m-80) REVERT: L 11 LEU cc_start: 0.8333 (mt) cc_final: 0.7950 (tt) REVERT: L 89 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6669 (tt0) outliers start: 71 outliers final: 46 residues processed: 271 average time/residue: 0.2290 time to fit residues: 92.5459 Evaluate side-chains 263 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN C 282 GLN C 295 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN G 208 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14020 Z= 0.251 Angle : 0.588 7.255 19032 Z= 0.308 Chirality : 0.045 0.401 2095 Planarity : 0.004 0.049 2451 Dihedral : 5.342 54.456 2253 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.60 % Allowed : 13.66 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.45 (0.20), residues: 1684 helix: 2.29 (0.27), residues: 363 sheet: 0.32 (0.31), residues: 261 loop : -0.41 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.004 0.001 HIS D 142 PHE 0.021 0.002 PHE G 118 TYR 0.025 0.002 TYR B 119 ARG 0.004 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 224 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8571 (t0) cc_final: 0.8299 (t0) REVERT: B 125 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7197 (tt0) REVERT: B 141 TYR cc_start: 0.6478 (m-80) cc_final: 0.5365 (m-80) REVERT: C 32 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7456 (mmmm) REVERT: C 225 ASP cc_start: 0.8004 (t0) cc_final: 0.7655 (t0) REVERT: D 45 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7462 (mp) REVERT: D 77 MET cc_start: 0.7124 (ttt) cc_final: 0.6911 (ttm) REVERT: D 142 HIS cc_start: 0.8118 (p90) cc_final: 0.7683 (p90) REVERT: G 179 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5568 (mt) REVERT: G 191 GLN cc_start: 0.8230 (tp40) cc_final: 0.7585 (tt0) REVERT: G 314 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5849 (mm) REVERT: G 320 LEU cc_start: 0.8650 (mp) cc_final: 0.8366 (mt) REVERT: I 109 ASP cc_start: 0.8468 (m-30) cc_final: 0.8094 (t70) REVERT: H 3 GLN cc_start: 0.7318 (mm-40) cc_final: 0.7082 (mm110) REVERT: H 100 PHE cc_start: 0.7246 (m-80) cc_final: 0.7039 (m-80) REVERT: L 11 LEU cc_start: 0.8379 (mt) cc_final: 0.8017 (tt) REVERT: L 89 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6770 (tt0) outliers start: 68 outliers final: 49 residues processed: 267 average time/residue: 0.2285 time to fit residues: 91.2695 Evaluate side-chains 264 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN D 25 HIS D 27 GLN G 208 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14020 Z= 0.248 Angle : 0.588 8.575 19032 Z= 0.307 Chirality : 0.045 0.404 2095 Planarity : 0.004 0.049 2451 Dihedral : 5.323 53.890 2253 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.73 % Allowed : 14.54 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.35 (0.20), residues: 1684 helix: 2.25 (0.27), residues: 363 sheet: 0.22 (0.31), residues: 261 loop : -0.48 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.004 0.001 HIS G 183 PHE 0.021 0.002 PHE G 118 TYR 0.025 0.002 TYR B 119 ARG 0.005 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 224 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8610 (t0) cc_final: 0.8343 (t0) REVERT: B 118 LEU cc_start: 0.8269 (tp) cc_final: 0.8032 (tp) REVERT: B 125 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7300 (tt0) REVERT: B 141 TYR cc_start: 0.6508 (m-80) cc_final: 0.5391 (m-80) REVERT: C 225 ASP cc_start: 0.7969 (t0) cc_final: 0.7556 (t0) REVERT: D 45 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7525 (mp) REVERT: D 77 MET cc_start: 0.7113 (ttt) cc_final: 0.6894 (ttm) REVERT: D 142 HIS cc_start: 0.8077 (p90) cc_final: 0.7692 (p90) REVERT: G 191 GLN cc_start: 0.8289 (tp40) cc_final: 0.7596 (tt0) REVERT: G 314 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5951 (mm) REVERT: I 109 ASP cc_start: 0.8357 (m-30) cc_final: 0.8050 (t70) REVERT: H 3 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7069 (mm110) REVERT: H 100 PHE cc_start: 0.7316 (m-80) cc_final: 0.6999 (m-80) REVERT: L 11 LEU cc_start: 0.8437 (mt) cc_final: 0.8069 (tt) REVERT: L 89 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6747 (tt0) outliers start: 70 outliers final: 57 residues processed: 269 average time/residue: 0.2250 time to fit residues: 91.4606 Evaluate side-chains 274 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 214 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN G 208 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14020 Z= 0.245 Angle : 0.600 8.621 19032 Z= 0.312 Chirality : 0.046 0.401 2095 Planarity : 0.004 0.048 2451 Dihedral : 5.552 55.920 2253 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.87 % Allowed : 14.94 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.28 (0.20), residues: 1684 helix: 2.21 (0.27), residues: 363 sheet: 0.11 (0.31), residues: 271 loop : -0.53 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.005 0.001 HIS B 26 PHE 0.022 0.002 PHE G 118 TYR 0.031 0.002 TYR A 17 ARG 0.006 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 227 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8656 (t0) cc_final: 0.8400 (t0) REVERT: A 32 LYS cc_start: 0.8859 (mttp) cc_final: 0.7883 (mmmt) REVERT: A 302 ILE cc_start: 0.7400 (mp) cc_final: 0.7193 (mp) REVERT: B 59 MET cc_start: 0.7179 (tpp) cc_final: 0.6731 (tpp) REVERT: B 118 LEU cc_start: 0.8304 (tp) cc_final: 0.8079 (tp) REVERT: B 125 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7341 (tt0) REVERT: B 137 CYS cc_start: 0.5785 (m) cc_final: 0.5415 (m) REVERT: B 141 TYR cc_start: 0.6610 (m-80) cc_final: 0.5455 (m-80) REVERT: C 105 TYR cc_start: 0.7579 (t80) cc_final: 0.7244 (t80) REVERT: C 225 ASP cc_start: 0.7978 (t0) cc_final: 0.7611 (t0) REVERT: D 45 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7530 (mp) REVERT: D 77 MET cc_start: 0.7123 (ttt) cc_final: 0.6893 (ttm) REVERT: D 119 TYR cc_start: 0.8574 (t80) cc_final: 0.8309 (t80) REVERT: D 142 HIS cc_start: 0.8114 (p90) cc_final: 0.7658 (p90) REVERT: G 245 PHE cc_start: 0.6368 (m-80) cc_final: 0.6083 (m-10) REVERT: G 314 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5771 (mm) REVERT: I 109 ASP cc_start: 0.8372 (m-30) cc_final: 0.7869 (t0) REVERT: H 3 GLN cc_start: 0.7312 (mm-40) cc_final: 0.7085 (mm110) REVERT: H 100 PHE cc_start: 0.7170 (m-80) cc_final: 0.6878 (m-80) REVERT: L 11 LEU cc_start: 0.8473 (mt) cc_final: 0.8085 (tt) REVERT: L 89 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6780 (tt0) outliers start: 72 outliers final: 54 residues processed: 271 average time/residue: 0.2339 time to fit residues: 94.6512 Evaluate side-chains 271 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 0.0370 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS I 125 GLN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14020 Z= 0.316 Angle : 0.643 9.713 19032 Z= 0.336 Chirality : 0.049 0.642 2095 Planarity : 0.004 0.053 2451 Dihedral : 5.903 57.885 2253 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.67 % Allowed : 15.89 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.06 (0.20), residues: 1684 helix: 2.05 (0.27), residues: 363 sheet: -0.03 (0.29), residues: 301 loop : -0.69 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.005 0.001 HIS G 183 PHE 0.026 0.002 PHE G 118 TYR 0.026 0.002 TYR B 119 ARG 0.007 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8749 (t0) cc_final: 0.8464 (t0) REVERT: A 32 LYS cc_start: 0.8834 (mttp) cc_final: 0.7910 (mmmt) REVERT: B 59 MET cc_start: 0.7143 (tpp) cc_final: 0.6679 (tpp) REVERT: B 118 LEU cc_start: 0.8308 (tp) cc_final: 0.8103 (tp) REVERT: B 125 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7445 (tt0) REVERT: B 137 CYS cc_start: 0.5840 (m) cc_final: 0.5420 (m) REVERT: B 141 TYR cc_start: 0.6685 (m-80) cc_final: 0.5444 (m-80) REVERT: C 225 ASP cc_start: 0.8077 (t0) cc_final: 0.7549 (t0) REVERT: C 226 GLN cc_start: 0.8229 (mm-40) cc_final: 0.8011 (mm110) REVERT: D 24 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: D 45 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7622 (mp) REVERT: D 77 MET cc_start: 0.7222 (ttt) cc_final: 0.6958 (ttm) REVERT: D 142 HIS cc_start: 0.8331 (p90) cc_final: 0.7712 (p90) REVERT: G 195 TYR cc_start: 0.8202 (m-80) cc_final: 0.7935 (m-10) REVERT: G 314 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5889 (mm) REVERT: I 109 ASP cc_start: 0.8394 (m-30) cc_final: 0.7930 (t0) REVERT: H 100 PHE cc_start: 0.7194 (m-80) cc_final: 0.6396 (m-80) REVERT: L 11 LEU cc_start: 0.8641 (mt) cc_final: 0.8265 (tt) REVERT: L 89 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6764 (tt0) outliers start: 69 outliers final: 55 residues processed: 258 average time/residue: 0.2273 time to fit residues: 88.9589 Evaluate side-chains 259 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 200 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 0.0570 chunk 150 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14020 Z= 0.187 Angle : 0.591 9.101 19032 Z= 0.304 Chirality : 0.046 0.469 2095 Planarity : 0.004 0.046 2451 Dihedral : 5.628 55.967 2253 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.11 % Allowed : 17.85 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.22 (0.20), residues: 1684 helix: 2.23 (0.27), residues: 363 sheet: 0.10 (0.30), residues: 301 loop : -0.62 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.007 0.001 HIS C 18 PHE 0.017 0.002 PHE G 118 TYR 0.024 0.001 TYR A 17 ARG 0.006 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8671 (t0) cc_final: 0.8382 (t0) REVERT: A 32 LYS cc_start: 0.8881 (mttp) cc_final: 0.7925 (mmmt) REVERT: A 155 THR cc_start: 0.7322 (p) cc_final: 0.7111 (m) REVERT: A 316 MET cc_start: 0.7419 (ttm) cc_final: 0.7198 (ttt) REVERT: B 59 MET cc_start: 0.7217 (tpp) cc_final: 0.6828 (tpp) REVERT: B 125 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7441 (tt0) REVERT: B 137 CYS cc_start: 0.5728 (m) cc_final: 0.5367 (m) REVERT: B 149 MET cc_start: 0.6742 (mtp) cc_final: 0.6479 (mtp) REVERT: C 18 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7713 (p-80) REVERT: C 225 ASP cc_start: 0.7968 (t0) cc_final: 0.7530 (t0) REVERT: C 226 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7781 (mm-40) REVERT: D 24 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: D 45 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7583 (mp) REVERT: D 77 MET cc_start: 0.7064 (ttt) cc_final: 0.6862 (ttm) REVERT: D 142 HIS cc_start: 0.8235 (p90) cc_final: 0.7649 (p90) REVERT: G 245 PHE cc_start: 0.6356 (m-80) cc_final: 0.6076 (m-10) REVERT: G 314 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5760 (mm) REVERT: I 109 ASP cc_start: 0.8288 (m-30) cc_final: 0.7925 (t0) REVERT: H 100 PHE cc_start: 0.7158 (m-80) cc_final: 0.6714 (m-80) REVERT: L 11 LEU cc_start: 0.8608 (mt) cc_final: 0.8195 (tt) outliers start: 46 outliers final: 35 residues processed: 255 average time/residue: 0.2160 time to fit residues: 83.4099 Evaluate side-chains 239 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 0.0980 chunk 141 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN G 208 HIS I 129 ASN I 142 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14020 Z= 0.324 Angle : 0.660 11.980 19032 Z= 0.341 Chirality : 0.048 0.444 2095 Planarity : 0.004 0.068 2451 Dihedral : 5.792 56.607 2253 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.31 % Allowed : 18.53 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.02 (0.20), residues: 1684 helix: 2.04 (0.27), residues: 363 sheet: -0.05 (0.30), residues: 301 loop : -0.79 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.008 0.001 HIS C 18 PHE 0.033 0.002 PHE L 98 TYR 0.028 0.002 TYR C 105 ARG 0.019 0.001 ARG B 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8748 (t0) cc_final: 0.8470 (t0) REVERT: A 32 LYS cc_start: 0.8967 (mttp) cc_final: 0.8024 (mmmt) REVERT: B 59 MET cc_start: 0.7239 (tpp) cc_final: 0.6873 (tpp) REVERT: B 125 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7349 (tt0) REVERT: B 137 CYS cc_start: 0.5651 (m) cc_final: 0.5326 (m) REVERT: B 141 TYR cc_start: 0.6778 (m-80) cc_final: 0.5563 (m-80) REVERT: C 18 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7639 (p-80) REVERT: C 225 ASP cc_start: 0.8065 (t0) cc_final: 0.7516 (t0) REVERT: C 226 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7854 (mm-40) REVERT: D 45 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7580 (mp) REVERT: D 77 MET cc_start: 0.7221 (ttt) cc_final: 0.6969 (ttm) REVERT: D 142 HIS cc_start: 0.8249 (p90) cc_final: 0.7603 (p90) REVERT: G 195 TYR cc_start: 0.8170 (m-80) cc_final: 0.7840 (m-10) REVERT: G 245 PHE cc_start: 0.6442 (m-80) cc_final: 0.6141 (m-10) REVERT: G 314 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5836 (mm) REVERT: I 109 ASP cc_start: 0.8343 (m-30) cc_final: 0.7920 (t0) REVERT: H 100 PHE cc_start: 0.7176 (m-80) cc_final: 0.6341 (m-80) REVERT: L 11 LEU cc_start: 0.8693 (mt) cc_final: 0.8240 (tt) outliers start: 49 outliers final: 40 residues processed: 234 average time/residue: 0.2119 time to fit residues: 76.4449 Evaluate side-chains 233 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN G 208 HIS I 129 ASN I 142 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.162021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138331 restraints weight = 21828.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.141571 restraints weight = 13745.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.143827 restraints weight = 9899.109| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14020 Z= 0.220 Angle : 0.637 14.707 19032 Z= 0.324 Chirality : 0.047 0.410 2095 Planarity : 0.004 0.075 2451 Dihedral : 5.720 56.744 2253 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.84 % Allowed : 19.34 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.07 (0.20), residues: 1684 helix: 2.15 (0.27), residues: 363 sheet: 0.04 (0.30), residues: 301 loop : -0.74 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.008 0.001 HIS C 18 PHE 0.028 0.002 PHE L 98 TYR 0.037 0.002 TYR D 162 ARG 0.016 0.001 ARG B 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2825.24 seconds wall clock time: 51 minutes 50.40 seconds (3110.40 seconds total)