Starting phenix.real_space_refine on Thu Feb 15 11:04:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2024/6y5g_10696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2024/6y5g_10696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2024/6y5g_10696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2024/6y5g_10696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2024/6y5g_10696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2024/6y5g_10696.pdb" } resolution = 3.0 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= 0.003 sd= 0.245 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 57 5.16 5 C 7482 2.51 5 N 2058 2.21 5 O 2439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F ASP 145": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12036 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 6.38, per 1000 atoms: 0.53 Number of scatterers: 12036 At special positions: 0 Unit cell: (87.2, 87.2, 150.42, 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 57 16.00 O 2439 8.00 N 2058 7.00 C 7482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.09 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.93 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=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.09 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 38 " " NAG A 410 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 38 " " NAG C 410 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 38 " " NAG E 410 " - " ASN E 81 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 285 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 285 " " NAG L 1 " - " ASN E 165 " " NAG M 1 " - " ASN E 285 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN F 154 " Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.2 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 24.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.578A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.690A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.579A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.690A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.578A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.689A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 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 52 removed outlier: 6.341A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.131A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.603A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.130A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC7, first strand: chain 'F' and resid 22 through 27 removed outlier: 3.815A pdb=" N ILE F 140 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.130A pdb=" N PHE E 87 " --> pdb=" O MET E 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS E 139 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY E 144 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 287 414 hydrogen bonds defined for protein. 1143 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: 3.67 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3966 1.34 - 1.46: 2924 1.46 - 1.58: 5308 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12276 Sorted by residual: bond pdb=" N ILE B 10 " pdb=" CA ILE B 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.13e+00 bond pdb=" N ILE F 10 " pdb=" CA ILE F 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N ILE D 10 " pdb=" CA ILE D 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N GLU D 11 " pdb=" CA GLU D 11 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.98e+00 bond pdb=" N GLU F 11 " pdb=" CA GLU F 11 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.96e+00 ... (remaining 12271 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.89: 345 106.89 - 113.67: 6977 113.67 - 120.44: 4414 120.44 - 127.22: 4785 127.22 - 133.99: 126 Bond angle restraints: 16647 Sorted by residual: angle pdb=" CA LYS D 39 " pdb=" CB LYS D 39 " pdb=" CG LYS D 39 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.28e+00 angle pdb=" CA LYS B 39 " pdb=" CB LYS B 39 " pdb=" CG LYS B 39 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" CA LYS F 39 " pdb=" CB LYS F 39 " pdb=" CG LYS F 39 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.11e+00 angle pdb=" O GLU B 85 " pdb=" C GLU B 85 " pdb=" N ASP B 86 " ideal model delta sigma weight residual 122.07 124.70 -2.63 1.03e+00 9.43e-01 6.53e+00 angle pdb=" O GLU F 85 " pdb=" C GLU F 85 " pdb=" N ASP F 86 " ideal model delta sigma weight residual 122.07 124.66 -2.59 1.03e+00 9.43e-01 6.31e+00 ... (remaining 16642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 7287 22.13 - 44.27: 411 44.27 - 66.40: 72 66.40 - 88.53: 42 88.53 - 110.66: 15 Dihedral angle restraints: 7827 sinusoidal: 3609 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.60 -79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.61 -79.39 1 1.00e+01 1.00e-02 7.83e+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 -86.00 -6.64 -79.36 1 1.00e+01 1.00e-02 7.83e+01 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 1920 0.314 - 0.627: 6 0.627 - 0.941: 3 0.941 - 1.255: 3 1.255 - 1.568: 3 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.15e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 ... (remaining 1932 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 74 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO E 74 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 73 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO C 74 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.026 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 886 2.73 - 3.27: 10349 3.27 - 3.82: 18279 3.82 - 4.36: 22695 4.36 - 4.90: 40185 Nonbonded interactions: 92394 Sorted by model distance: nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.189 2.520 nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.189 2.520 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.189 2.520 nonbonded pdb=" OE1 GLU F 131 " pdb=" OH TYR F 141 " model vdw 2.280 2.440 nonbonded pdb=" OE1 GLU B 131 " pdb=" OH TYR B 141 " model vdw 2.280 2.440 ... (remaining 92389 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 13.160 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.420 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.005 0.033 12276 Z= 0.343 Angle : 0.661 6.670 16647 Z= 0.345 Chirality : 0.101 1.568 1935 Planarity : 0.004 0.047 2130 Dihedral : 15.738 110.663 5067 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.94 % Allowed : 12.65 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.18), residues: 1458 helix: -0.38 (0.26), residues: 366 sheet: -1.23 (0.33), residues: 228 loop : -3.05 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 PHE 0.013 0.001 PHE F 9 TYR 0.010 0.001 TYR E 161 ARG 0.002 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 111 LEU cc_start: 0.8585 (tt) cc_final: 0.8270 (tp) REVERT: A 119 GLU cc_start: 0.8087 (tt0) cc_final: 0.7866 (tt0) REVERT: B 46 ASP cc_start: 0.7800 (m-30) cc_final: 0.7480 (m-30) REVERT: C 62 ILE cc_start: 0.8819 (mt) cc_final: 0.8579 (mp) REVERT: C 82 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8093 (mm-30) REVERT: E 27 LYS cc_start: 0.8307 (mttt) cc_final: 0.7933 (mtmm) REVERT: E 111 LEU cc_start: 0.8684 (tt) cc_final: 0.8319 (tt) REVERT: E 119 GLU cc_start: 0.8184 (tt0) cc_final: 0.7955 (tt0) REVERT: E 139 CYS cc_start: 0.7879 (t) cc_final: 0.7368 (t) REVERT: D 49 ASN cc_start: 0.7872 (m-40) cc_final: 0.7542 (m-40) REVERT: D 62 LYS cc_start: 0.8304 (mttt) cc_final: 0.7958 (mmtt) REVERT: D 115 MET cc_start: 0.8653 (tpt) cc_final: 0.8397 (mmm) REVERT: D 121 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7449 (ttmm) REVERT: D 139 LYS cc_start: 0.8239 (tttp) cc_final: 0.7941 (tptm) REVERT: F 115 MET cc_start: 0.8851 (tpt) cc_final: 0.8648 (mmm) REVERT: F 139 LYS cc_start: 0.8220 (tttp) cc_final: 0.7976 (tptm) REVERT: F 168 ASN cc_start: 0.7901 (t0) cc_final: 0.7488 (m-40) outliers start: 12 outliers final: 0 residues processed: 237 average time/residue: 1.4410 time to fit residues: 366.6198 Evaluate side-chains 166 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 125 GLN C 33 GLN C 216 ASN E 17 HIS ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12276 Z= 0.388 Angle : 0.658 7.122 16647 Z= 0.336 Chirality : 0.050 0.225 1935 Planarity : 0.005 0.045 2130 Dihedral : 11.119 95.266 2322 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.43 % Allowed : 15.46 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1458 helix: 0.51 (0.28), residues: 375 sheet: -0.77 (0.33), residues: 228 loop : -2.58 (0.16), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 75 PHE 0.023 0.002 PHE D 9 TYR 0.014 0.002 TYR C 308 ARG 0.009 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 183 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 77 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6884 (t0) REVERT: A 111 LEU cc_start: 0.8672 (tt) cc_final: 0.8379 (tp) REVERT: A 321 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7649 (ttt180) REVERT: B 54 ARG cc_start: 0.7947 (tpt90) cc_final: 0.5579 (tmt-80) REVERT: B 72 GLU cc_start: 0.7483 (mp0) cc_final: 0.7085 (mp0) REVERT: C 41 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: C 62 ILE cc_start: 0.8814 (mt) cc_final: 0.8555 (mp) REVERT: C 82 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 321 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7583 (ttt180) REVERT: E 27 LYS cc_start: 0.8286 (mttt) cc_final: 0.7862 (mtmm) REVERT: E 41 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: E 70 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8293 (tp) REVERT: E 111 LEU cc_start: 0.8648 (tt) cc_final: 0.8327 (tt) REVERT: E 139 CYS cc_start: 0.7692 (t) cc_final: 0.7198 (t) REVERT: E 321 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7504 (ttt180) REVERT: D 49 ASN cc_start: 0.7966 (m-40) cc_final: 0.7655 (m-40) REVERT: D 62 LYS cc_start: 0.8255 (mttt) cc_final: 0.7952 (mmtt) REVERT: D 115 MET cc_start: 0.8735 (tpt) cc_final: 0.8491 (mmm) REVERT: D 121 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7433 (ttmm) REVERT: D 139 LYS cc_start: 0.8364 (tttp) cc_final: 0.8036 (tptm) REVERT: D 164 ASP cc_start: 0.7266 (p0) cc_final: 0.7054 (p0) REVERT: F 37 ASP cc_start: 0.7896 (t0) cc_final: 0.7600 (t70) REVERT: F 115 MET cc_start: 0.8881 (tpt) cc_final: 0.8501 (mmm) REVERT: F 160 ASP cc_start: 0.8079 (m-30) cc_final: 0.7867 (m-30) REVERT: F 168 ASN cc_start: 0.7956 (t0) cc_final: 0.7481 (m-40) outliers start: 44 outliers final: 20 residues processed: 204 average time/residue: 1.3709 time to fit residues: 301.4401 Evaluate side-chains 191 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 105 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 216 ASN C 246 ASN E 54 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12276 Z= 0.243 Angle : 0.560 7.150 16647 Z= 0.292 Chirality : 0.046 0.230 1935 Planarity : 0.004 0.040 2130 Dihedral : 10.010 87.423 2322 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.29 % Allowed : 15.46 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1458 helix: 1.43 (0.29), residues: 354 sheet: -0.18 (0.36), residues: 204 loop : -2.23 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE B 9 TYR 0.008 0.001 TYR C 308 ARG 0.008 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 170 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 77 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6949 (t0) REVERT: A 111 LEU cc_start: 0.8651 (tt) cc_final: 0.8351 (tp) REVERT: A 280 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: A 321 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7658 (ttt180) REVERT: B 54 ARG cc_start: 0.7907 (tpt90) cc_final: 0.5597 (tmt-80) REVERT: B 72 GLU cc_start: 0.7356 (mp0) cc_final: 0.6991 (mp0) REVERT: C 41 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: C 82 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 321 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7672 (ttt180) REVERT: E 27 LYS cc_start: 0.8247 (mttt) cc_final: 0.7831 (mtmm) REVERT: E 31 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6691 (t0) REVERT: E 41 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: E 111 LEU cc_start: 0.8694 (tt) cc_final: 0.8396 (tt) REVERT: E 139 CYS cc_start: 0.7833 (t) cc_final: 0.7347 (t) REVERT: E 321 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7513 (ttt180) REVERT: D 38 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7503 (mt) REVERT: D 49 ASN cc_start: 0.7910 (m-40) cc_final: 0.7587 (m-40) REVERT: D 62 LYS cc_start: 0.8247 (mttt) cc_final: 0.7972 (mmtt) REVERT: D 120 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: D 121 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7464 (ttmm) REVERT: D 139 LYS cc_start: 0.8369 (tttp) cc_final: 0.7923 (tptm) REVERT: F 37 ASP cc_start: 0.7868 (t0) cc_final: 0.7566 (t70) REVERT: F 115 MET cc_start: 0.8876 (tpt) cc_final: 0.8530 (mmm) REVERT: F 121 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7371 (tttp) REVERT: F 123 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7726 (ttp80) REVERT: F 139 LYS cc_start: 0.8423 (tttm) cc_final: 0.7997 (tptm) REVERT: F 168 ASN cc_start: 0.7942 (t0) cc_final: 0.7446 (m-40) outliers start: 55 outliers final: 25 residues processed: 206 average time/residue: 1.3372 time to fit residues: 297.5797 Evaluate side-chains 198 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 216 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12276 Z= 0.306 Angle : 0.601 9.040 16647 Z= 0.311 Chirality : 0.048 0.264 1935 Planarity : 0.004 0.039 2130 Dihedral : 9.322 80.776 2322 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.98 % Allowed : 16.47 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1458 helix: 1.49 (0.29), residues: 357 sheet: -0.07 (0.36), residues: 204 loop : -2.12 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 PHE 0.019 0.002 PHE D 9 TYR 0.009 0.002 TYR C 308 ARG 0.009 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: A 77 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6922 (t0) REVERT: A 111 LEU cc_start: 0.8670 (tt) cc_final: 0.8383 (tp) REVERT: A 280 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: B 72 GLU cc_start: 0.7332 (mp0) cc_final: 0.6927 (mp0) REVERT: C 41 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: C 70 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8204 (tp) REVERT: C 82 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 321 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7664 (ttt180) REVERT: E 27 LYS cc_start: 0.8282 (mttt) cc_final: 0.7882 (mtmm) REVERT: E 31 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6754 (t0) REVERT: E 41 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: E 70 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8264 (tp) REVERT: E 111 LEU cc_start: 0.8691 (tt) cc_final: 0.8386 (tt) REVERT: E 321 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7524 (ttt180) REVERT: D 38 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7573 (mt) REVERT: D 49 ASN cc_start: 0.7952 (m-40) cc_final: 0.7636 (m-40) REVERT: D 62 LYS cc_start: 0.8237 (mttt) cc_final: 0.7965 (mmtt) REVERT: D 121 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7485 (ttmm) REVERT: D 139 LYS cc_start: 0.8446 (tttp) cc_final: 0.8079 (tptm) REVERT: F 37 ASP cc_start: 0.7821 (t0) cc_final: 0.7537 (t70) REVERT: F 115 MET cc_start: 0.8868 (tpt) cc_final: 0.8503 (mmm) REVERT: F 121 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7376 (tttp) REVERT: F 168 ASN cc_start: 0.7993 (t0) cc_final: 0.7480 (m-40) outliers start: 51 outliers final: 27 residues processed: 188 average time/residue: 1.3690 time to fit residues: 277.9201 Evaluate side-chains 194 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12276 Z= 0.320 Angle : 0.650 20.785 16647 Z= 0.335 Chirality : 0.050 0.362 1935 Planarity : 0.004 0.041 2130 Dihedral : 8.744 74.014 2322 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.14 % Allowed : 16.86 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1458 helix: 1.56 (0.28), residues: 357 sheet: -0.05 (0.36), residues: 204 loop : -2.06 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 234 HIS 0.004 0.001 HIS A 75 PHE 0.019 0.002 PHE D 9 TYR 0.010 0.002 TYR C 308 ARG 0.009 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 153 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 77 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6954 (t0) REVERT: A 111 LEU cc_start: 0.8694 (tt) cc_final: 0.8418 (tp) REVERT: A 280 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: B 72 GLU cc_start: 0.7327 (mp0) cc_final: 0.6920 (mp0) REVERT: C 41 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: C 70 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8202 (tp) REVERT: C 173 ASN cc_start: 0.8596 (p0) cc_final: 0.8393 (p0) REVERT: C 321 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7644 (ttt180) REVERT: E 27 LYS cc_start: 0.8270 (mttt) cc_final: 0.7867 (mtmm) REVERT: E 31 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6703 (t0) REVERT: E 41 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: E 70 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8271 (tp) REVERT: E 111 LEU cc_start: 0.8677 (tt) cc_final: 0.8379 (tt) REVERT: E 321 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7525 (ttt180) REVERT: D 38 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7571 (mt) REVERT: D 49 ASN cc_start: 0.7944 (m-40) cc_final: 0.7638 (m-40) REVERT: D 62 LYS cc_start: 0.8257 (mttt) cc_final: 0.8019 (mmtt) REVERT: D 120 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: D 121 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7512 (ttmm) REVERT: D 139 LYS cc_start: 0.8378 (tttp) cc_final: 0.8076 (tptm) REVERT: D 168 ASN cc_start: 0.8100 (t0) cc_final: 0.7411 (t0) REVERT: F 115 MET cc_start: 0.8858 (tpt) cc_final: 0.8490 (mmm) REVERT: F 139 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8304 (tptm) REVERT: F 168 ASN cc_start: 0.8110 (t0) cc_final: 0.7484 (m-40) outliers start: 53 outliers final: 30 residues processed: 190 average time/residue: 1.2972 time to fit residues: 266.3621 Evaluate side-chains 192 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12276 Z= 0.259 Angle : 0.639 19.078 16647 Z= 0.330 Chirality : 0.050 0.374 1935 Planarity : 0.004 0.045 2130 Dihedral : 7.976 65.312 2322 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 17.10 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1458 helix: 1.74 (0.29), residues: 357 sheet: -0.00 (0.35), residues: 204 loop : -1.99 (0.17), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 PHE 0.016 0.002 PHE D 9 TYR 0.007 0.001 TYR C 308 ARG 0.010 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 77 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6954 (t0) REVERT: A 111 LEU cc_start: 0.8677 (tt) cc_final: 0.8422 (tp) REVERT: A 280 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: B 72 GLU cc_start: 0.7276 (mp0) cc_final: 0.6954 (mp0) REVERT: C 41 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: C 70 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8185 (tp) REVERT: C 321 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7643 (ttt180) REVERT: E 27 LYS cc_start: 0.8257 (mttt) cc_final: 0.7927 (mtmm) REVERT: E 31 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6800 (t0) REVERT: E 41 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: E 70 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8385 (tp) REVERT: E 111 LEU cc_start: 0.8689 (tt) cc_final: 0.8402 (tt) REVERT: E 321 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7559 (ttt180) REVERT: D 38 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7569 (mt) REVERT: D 49 ASN cc_start: 0.7934 (m-40) cc_final: 0.7622 (m-40) REVERT: D 62 LYS cc_start: 0.8233 (mttt) cc_final: 0.7989 (mmtt) REVERT: D 121 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7512 (ttmm) REVERT: D 139 LYS cc_start: 0.8324 (tttp) cc_final: 0.8054 (tptm) REVERT: D 168 ASN cc_start: 0.8112 (t0) cc_final: 0.7370 (t0) REVERT: F 115 MET cc_start: 0.8854 (tpt) cc_final: 0.8471 (mmm) REVERT: F 139 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8283 (tptm) REVERT: F 168 ASN cc_start: 0.8107 (t0) cc_final: 0.7456 (m-40) outliers start: 52 outliers final: 34 residues processed: 192 average time/residue: 1.2849 time to fit residues: 267.0818 Evaluate side-chains 199 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.0010 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12276 Z= 0.204 Angle : 0.599 18.547 16647 Z= 0.310 Chirality : 0.047 0.330 1935 Planarity : 0.004 0.048 2130 Dihedral : 7.161 55.415 2322 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.90 % Allowed : 17.64 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.81 (0.20), residues: 1458 helix: 2.01 (0.29), residues: 354 sheet: 0.11 (0.35), residues: 204 loop : -1.89 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 234 HIS 0.003 0.001 HIS F 106 PHE 0.014 0.001 PHE D 9 TYR 0.007 0.001 TYR B 162 ARG 0.010 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6943 (t0) REVERT: A 111 LEU cc_start: 0.8601 (tt) cc_final: 0.8358 (tp) REVERT: A 280 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: B 72 GLU cc_start: 0.7193 (mp0) cc_final: 0.6809 (mp0) REVERT: C 31 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: C 41 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: C 62 ILE cc_start: 0.8546 (mt) cc_final: 0.8198 (mp) REVERT: C 70 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8168 (tp) REVERT: C 77 ASP cc_start: 0.7345 (m-30) cc_final: 0.7067 (t0) REVERT: C 321 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7617 (ttt180) REVERT: E 27 LYS cc_start: 0.8233 (mttt) cc_final: 0.7896 (mtmm) REVERT: E 41 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: E 70 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8342 (tp) REVERT: E 111 LEU cc_start: 0.8682 (tt) cc_final: 0.8446 (tp) REVERT: E 321 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7557 (ttt180) REVERT: D 38 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7497 (mt) REVERT: D 49 ASN cc_start: 0.7885 (m-40) cc_final: 0.7562 (m-40) REVERT: D 62 LYS cc_start: 0.8224 (mttt) cc_final: 0.7984 (mmtt) REVERT: D 72 GLU cc_start: 0.7422 (mp0) cc_final: 0.6839 (mp0) REVERT: D 121 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7441 (ttmm) REVERT: D 139 LYS cc_start: 0.8283 (tttp) cc_final: 0.7992 (tptm) REVERT: D 168 ASN cc_start: 0.8073 (t0) cc_final: 0.7358 (t0) REVERT: F 57 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6553 (pt0) REVERT: F 115 MET cc_start: 0.8866 (tpt) cc_final: 0.8421 (mmm) REVERT: F 168 ASN cc_start: 0.8140 (t0) cc_final: 0.7458 (m-40) outliers start: 50 outliers final: 31 residues processed: 191 average time/residue: 1.2964 time to fit residues: 267.8706 Evaluate side-chains 191 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12276 Z= 0.281 Angle : 0.654 19.029 16647 Z= 0.336 Chirality : 0.049 0.357 1935 Planarity : 0.004 0.047 2130 Dihedral : 7.050 53.097 2322 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.06 % Allowed : 17.72 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.86 (0.21), residues: 1458 helix: 1.95 (0.29), residues: 354 sheet: -0.18 (0.32), residues: 255 loop : -1.93 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.004 0.001 HIS A 75 PHE 0.017 0.002 PHE D 9 TYR 0.010 0.001 TYR C 308 ARG 0.010 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6961 (t0) REVERT: A 111 LEU cc_start: 0.8625 (tt) cc_final: 0.8377 (tp) REVERT: A 280 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: B 72 GLU cc_start: 0.7212 (mp0) cc_final: 0.6822 (mp0) REVERT: C 31 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6816 (m-30) REVERT: C 41 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: C 70 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8216 (tp) REVERT: C 321 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7627 (ttt180) REVERT: E 27 LYS cc_start: 0.8259 (mttt) cc_final: 0.7917 (mtmm) REVERT: E 41 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: E 70 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8364 (tp) REVERT: E 111 LEU cc_start: 0.8699 (tt) cc_final: 0.8407 (tt) REVERT: E 321 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7562 (ttt180) REVERT: D 38 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7532 (mt) REVERT: D 49 ASN cc_start: 0.7950 (m-40) cc_final: 0.7642 (m-40) REVERT: D 62 LYS cc_start: 0.8239 (mttt) cc_final: 0.8009 (mmtt) REVERT: D 72 GLU cc_start: 0.7435 (mp0) cc_final: 0.6847 (mp0) REVERT: D 121 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7455 (ttmm) REVERT: D 139 LYS cc_start: 0.8318 (tttp) cc_final: 0.7986 (tptm) REVERT: D 168 ASN cc_start: 0.8116 (t0) cc_final: 0.7406 (t0) REVERT: F 57 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6571 (pt0) REVERT: F 115 MET cc_start: 0.8860 (tpt) cc_final: 0.8414 (mmm) REVERT: F 121 LYS cc_start: 0.7803 (tttt) cc_final: 0.7339 (tttp) REVERT: F 139 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8178 (tptm) REVERT: F 168 ASN cc_start: 0.8154 (t0) cc_final: 0.7464 (m-40) outliers start: 52 outliers final: 38 residues processed: 186 average time/residue: 1.2788 time to fit residues: 257.1623 Evaluate side-chains 196 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12276 Z= 0.287 Angle : 0.648 17.498 16647 Z= 0.335 Chirality : 0.049 0.335 1935 Planarity : 0.004 0.047 2130 Dihedral : 6.868 49.758 2322 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.06 % Allowed : 18.35 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.88 (0.21), residues: 1458 helix: 1.92 (0.29), residues: 354 sheet: -0.19 (0.32), residues: 255 loop : -1.93 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 PHE 0.017 0.002 PHE D 9 TYR 0.009 0.001 TYR C 308 ARG 0.010 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6963 (t0) REVERT: A 111 LEU cc_start: 0.8645 (tt) cc_final: 0.8398 (tp) REVERT: A 280 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: B 34 GLN cc_start: 0.9057 (tt0) cc_final: 0.8852 (tt0) REVERT: B 72 GLU cc_start: 0.7208 (mp0) cc_final: 0.6853 (mp0) REVERT: C 31 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: C 41 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: C 70 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8209 (tp) REVERT: C 77 ASP cc_start: 0.7370 (m-30) cc_final: 0.7083 (t0) REVERT: C 119 GLU cc_start: 0.8130 (tt0) cc_final: 0.7830 (tt0) REVERT: C 321 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7616 (ttt180) REVERT: E 27 LYS cc_start: 0.8263 (mttt) cc_final: 0.7915 (mtmm) REVERT: E 41 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6705 (tm-30) REVERT: E 70 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8369 (tp) REVERT: E 111 LEU cc_start: 0.8669 (tt) cc_final: 0.8382 (tt) REVERT: E 321 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7568 (ttt180) REVERT: D 38 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7542 (mt) REVERT: D 49 ASN cc_start: 0.7947 (m-40) cc_final: 0.7649 (m-40) REVERT: D 62 LYS cc_start: 0.8259 (mttt) cc_final: 0.8010 (mmtt) REVERT: D 72 GLU cc_start: 0.7436 (mp0) cc_final: 0.6834 (mp0) REVERT: D 121 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7526 (ttmm) REVERT: D 139 LYS cc_start: 0.8374 (tttp) cc_final: 0.8014 (tptm) REVERT: D 168 ASN cc_start: 0.8117 (t0) cc_final: 0.7412 (t0) REVERT: F 57 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6584 (pt0) REVERT: F 115 MET cc_start: 0.8862 (tpt) cc_final: 0.8435 (mmm) REVERT: F 121 LYS cc_start: 0.7788 (tttt) cc_final: 0.7328 (tttp) REVERT: F 139 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8149 (tptm) outliers start: 52 outliers final: 38 residues processed: 189 average time/residue: 1.2961 time to fit residues: 265.1010 Evaluate side-chains 195 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 146 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12276 Z= 0.266 Angle : 0.636 16.950 16647 Z= 0.328 Chirality : 0.048 0.322 1935 Planarity : 0.004 0.043 2130 Dihedral : 6.685 47.612 2322 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.83 % Allowed : 18.81 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.85 (0.21), residues: 1458 helix: 1.96 (0.29), residues: 354 sheet: -0.17 (0.32), residues: 255 loop : -1.92 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 PHE 0.016 0.002 PHE D 9 TYR 0.008 0.001 TYR C 308 ARG 0.010 0.001 ARG A 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 146 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6965 (t0) REVERT: A 111 LEU cc_start: 0.8638 (tt) cc_final: 0.8393 (tp) REVERT: A 280 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: B 34 GLN cc_start: 0.9056 (tt0) cc_final: 0.8848 (tt0) REVERT: B 72 GLU cc_start: 0.7148 (mp0) cc_final: 0.6843 (mp0) REVERT: C 31 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: C 41 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: C 70 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8199 (tp) REVERT: C 77 ASP cc_start: 0.7352 (m-30) cc_final: 0.7078 (t0) REVERT: C 321 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7631 (ttt180) REVERT: E 27 LYS cc_start: 0.8257 (mttt) cc_final: 0.7909 (mtmm) REVERT: E 41 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: E 70 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8376 (tp) REVERT: E 111 LEU cc_start: 0.8699 (tt) cc_final: 0.8424 (tt) REVERT: E 321 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7566 (ttt180) REVERT: D 38 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7533 (mt) REVERT: D 49 ASN cc_start: 0.7938 (m-40) cc_final: 0.7622 (m-40) REVERT: D 62 LYS cc_start: 0.8227 (mttt) cc_final: 0.7975 (mmtt) REVERT: D 72 GLU cc_start: 0.7397 (mp0) cc_final: 0.6830 (mp0) REVERT: D 121 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7459 (ttmm) REVERT: D 139 LYS cc_start: 0.8372 (tttp) cc_final: 0.8000 (tptm) REVERT: D 168 ASN cc_start: 0.8119 (t0) cc_final: 0.7412 (t0) REVERT: F 57 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6589 (pt0) REVERT: F 115 MET cc_start: 0.8861 (tpt) cc_final: 0.8442 (mmm) REVERT: F 121 LYS cc_start: 0.7828 (tttt) cc_final: 0.7354 (tttp) REVERT: F 139 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8138 (tptm) outliers start: 49 outliers final: 36 residues processed: 182 average time/residue: 1.3057 time to fit residues: 256.9117 Evaluate side-chains 194 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 145 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 105 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.103408 restraints weight = 14233.394| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.85 r_work: 0.2956 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12276 Z= 0.147 Angle : 0.569 15.229 16647 Z= 0.294 Chirality : 0.046 0.311 1935 Planarity : 0.004 0.041 2130 Dihedral : 6.357 45.017 2322 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.73 % Allowed : 19.75 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.62 (0.21), residues: 1458 helix: 2.25 (0.29), residues: 354 sheet: 0.11 (0.36), residues: 204 loop : -1.78 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 92 HIS 0.002 0.001 HIS D 106 PHE 0.011 0.001 PHE E 120 TYR 0.006 0.001 TYR C 105 ARG 0.010 0.000 ARG A 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.95 seconds wall clock time: 84 minutes 45.97 seconds (5085.97 seconds total)