Starting phenix.real_space_refine on Thu Feb 15 10:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2024/6y5h_10697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2024/6y5h_10697.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/6y5h_10697/02_2024/6y5h_10697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2024/6y5h_10697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2024/6y5h_10697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2024/6y5h_10697.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= 0.253 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 7458 2.51 5 N 2055 2.21 5 O 2424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "C ASP 31": "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 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 158": "OD1" <-> "OD2" Residue "F ASP 160": "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: 11994 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: 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: "C" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.67, per 1000 atoms: 0.56 Number of scatterers: 11994 At special positions: 0 Unit cell: (86.11, 87.2, 149.33, 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 2424 8.00 N 2055 7.00 C 7458 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=2.11 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=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.96 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 38 " " NAG A 409 " - " ASN A 81 " " NAG C 401 " - " ASN C 38 " " NAG C 409 " - " ASN C 81 " " NAG E 401 " - " ASN E 38 " " NAG E 409 " - " 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: 5.12 Conformation dependent library (CDL) restraints added in 2.4 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: 27 helices and 33 sheets defined 26.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.801A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.154A 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 76 through 80 removed outlier: 3.815A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.778A pdb=" N VAL D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.647A pdb=" N GLN F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 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: 6.064A 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: 6.691A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.066A 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 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.517A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.690A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.687A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 286 through 287 427 hydrogen bonds defined for protein. 1173 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: 3.50 Time building geometry restraints manager: 5.49 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: 3868 1.34 - 1.46: 2158 1.46 - 1.58: 6130 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 12234 Sorted by residual: bond pdb=" N PHE E 79 " pdb=" CA PHE E 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.76e+00 bond pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.75e+00 bond pdb=" N GLN E 80 " pdb=" CA GLN E 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N ILE C 214 " pdb=" CA ILE C 214 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.53e+00 bond pdb=" N GLN A 80 " pdb=" CA GLN A 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.48e+00 ... (remaining 12229 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.26: 431 107.26 - 113.98: 7003 113.98 - 120.69: 4651 120.69 - 127.41: 4386 127.41 - 134.13: 119 Bond angle restraints: 16590 Sorted by residual: angle pdb=" CA ASN E 81 " pdb=" C ASN E 81 " pdb=" O ASN E 81 " ideal model delta sigma weight residual 121.28 117.58 3.70 1.19e+00 7.06e-01 9.68e+00 angle pdb=" CA ASN C 81 " pdb=" C ASN C 81 " pdb=" O ASN C 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.58e+00 angle pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" O ASN A 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.55e+00 angle pdb=" C VAL A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 122.83 118.65 4.18 1.54e+00 4.22e-01 7.38e+00 angle pdb=" C VAL C 78 " pdb=" N PHE C 79 " pdb=" CA PHE C 79 " ideal model delta sigma weight residual 122.83 118.66 4.17 1.54e+00 4.22e-01 7.34e+00 ... (remaining 16585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 7103 22.03 - 44.07: 529 44.07 - 66.10: 75 66.10 - 88.14: 39 88.14 - 110.17: 18 Dihedral angle restraints: 7764 sinusoidal: 3546 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.54 89.46 1 1.00e+01 1.00e-02 9.51e+01 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 93.00 3.60 89.40 1 1.00e+01 1.00e-02 9.50e+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 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 7761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1905 0.236 - 0.472: 6 0.472 - 0.708: 6 0.708 - 0.943: 0 0.943 - 1.179: 3 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.46e+03 ... (remaining 1917 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.38e+02 pdb=" C7 NAG E 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 409 " 0.223 2.00e-02 2.50e+03 pdb=" O7 NAG E 409 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG A 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG A 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG A 409 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG C 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG C 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG C 409 " 0.022 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1954 2.77 - 3.30: 9864 3.30 - 3.84: 18906 3.84 - 4.37: 22571 4.37 - 4.90: 40324 Nonbonded interactions: 93619 Sorted by model distance: nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.238 2.520 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.238 2.520 nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.239 2.520 nonbonded pdb=" OD1 ASP C 68 " pdb=" OH TYR C 100 " model vdw 2.337 2.440 nonbonded pdb=" OD1 ASP E 68 " pdb=" OH TYR E 100 " model vdw 2.337 2.440 ... (remaining 93614 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: 3.410 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: 13.300 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.200 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 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 : 0.004 0.034 12234 Z= 0.230 Angle : 0.655 6.184 16590 Z= 0.351 Chirality : 0.076 1.179 1920 Planarity : 0.007 0.138 2127 Dihedral : 16.337 110.171 5004 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.70 % Allowed : 16.39 % Favored : 82.90 % 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: -2.50 (0.18), residues: 1458 helix: -0.26 (0.26), residues: 348 sheet: -0.34 (0.31), residues: 243 loop : -2.83 (0.15), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 84 HIS 0.004 0.001 HIS F 142 PHE 0.007 0.001 PHE F 9 TYR 0.005 0.001 TYR C 161 ARG 0.004 0.000 ARG D 124 *********************** 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 276 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 267 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 274 average time/residue: 1.0372 time to fit residues: 314.1786 Evaluate side-chains 140 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 84 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 216 ASN B 27 GLN C 18 HIS C 54 ASN C 132 GLN C 197 GLN C 211 GLN E 54 ASN E 132 GLN E 188 ASN D 146 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 12234 Z= 0.428 Angle : 1.025 12.553 16590 Z= 0.503 Chirality : 0.065 0.692 1920 Planarity : 0.007 0.064 2127 Dihedral : 9.713 68.557 2262 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.71 % Allowed : 18.50 % Favored : 74.79 % 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: -1.84 (0.19), residues: 1458 helix: -0.30 (0.25), residues: 360 sheet: -0.15 (0.33), residues: 258 loop : -2.08 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 153 HIS 0.010 0.002 HIS C 75 PHE 0.025 0.003 PHE D 63 TYR 0.038 0.003 TYR B 162 ARG 0.013 0.001 ARG F 153 *********************** 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 314 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 228 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 290 ASN cc_start: 0.7129 (p0) cc_final: 0.6839 (p0) REVERT: B 65 GLN cc_start: 0.8103 (mt0) cc_final: 0.7799 (mt0) REVERT: B 121 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7711 (ttpt) REVERT: C 277 CYS cc_start: 0.5521 (OUTLIER) cc_final: 0.5164 (p) REVERT: C 310 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8152 (mtpt) REVERT: E 168 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7382 (tpt) REVERT: E 207 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7217 (mtt180) REVERT: E 241 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7725 (t0) REVERT: E 292 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8423 (mttm) REVERT: D 62 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7070 (mtpp) REVERT: D 65 GLN cc_start: 0.8416 (mt0) cc_final: 0.8141 (mt0) REVERT: F 17 MET cc_start: 0.8349 (tpp) cc_final: 0.8129 (ttm) REVERT: F 45 ILE cc_start: 0.8195 (tt) cc_final: 0.7791 (pp) REVERT: F 59 THR cc_start: 0.4183 (OUTLIER) cc_final: 0.3871 (p) outliers start: 86 outliers final: 19 residues processed: 295 average time/residue: 1.1094 time to fit residues: 356.5072 Evaluate side-chains 183 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 59 THR 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: 0.9980 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 34 GLN C 18 HIS C 248 ASN E 18 HIS E 191 GLN D 47 GLN D 105 GLN D 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.8844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12234 Z= 0.333 Angle : 0.695 9.565 16590 Z= 0.354 Chirality : 0.050 0.272 1920 Planarity : 0.006 0.051 2127 Dihedral : 9.167 78.577 2259 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.62 % Allowed : 22.33 % Favored : 72.05 % 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: -1.29 (0.20), residues: 1458 helix: 1.02 (0.28), residues: 357 sheet: 0.19 (0.33), residues: 234 loop : -2.11 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.009 0.002 HIS D 142 PHE 0.024 0.002 PHE B 24 TYR 0.020 0.002 TYR A 308 ARG 0.005 0.001 ARG C 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 239 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 167 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 CYS cc_start: 0.6915 (m) cc_final: 0.6503 (m) REVERT: A 168 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8047 (tpt) REVERT: A 243 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8466 (tp) REVERT: A 275 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6377 (t0) REVERT: B 46 ASP cc_start: 0.7260 (m-30) cc_final: 0.7035 (m-30) REVERT: B 47 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: B 67 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: B 121 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7779 (ttpt) REVERT: C 89 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: C 145 SER cc_start: 0.7818 (m) cc_final: 0.7441 (p) REVERT: C 168 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7773 (mmp) REVERT: C 210 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: C 243 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8306 (tp) REVERT: C 245 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.7950 (mt) REVERT: E 168 MET cc_start: 0.8192 (mmt) cc_final: 0.7971 (mmt) REVERT: E 207 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8034 (mtm-85) REVERT: E 223 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8480 (t) REVERT: E 275 ASP cc_start: 0.7007 (p0) cc_final: 0.6770 (p0) REVERT: F 17 MET cc_start: 0.8512 (tpp) cc_final: 0.8184 (ttm) REVERT: F 151 SER cc_start: 0.7274 (t) cc_final: 0.6673 (p) outliers start: 72 outliers final: 25 residues processed: 219 average time/residue: 1.0019 time to fit residues: 242.0008 Evaluate side-chains 181 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 30 GLU 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: 0.7980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 197 GLN E 295 GLN D 47 GLN D 105 GLN F 28 ASN F 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.9776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12234 Z= 0.328 Angle : 0.641 9.528 16590 Z= 0.333 Chirality : 0.049 0.304 1920 Planarity : 0.005 0.047 2127 Dihedral : 8.207 68.537 2259 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.31 % Allowed : 22.87 % Favored : 71.82 % 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: -1.09 (0.20), residues: 1458 helix: 1.22 (0.28), residues: 357 sheet: 0.37 (0.34), residues: 234 loop : -2.02 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.008 0.002 HIS A 75 PHE 0.019 0.002 PHE C 125 TYR 0.017 0.002 TYR A 308 ARG 0.007 0.001 ARG B 153 *********************** 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 232 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 164 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8127 (tpt) REVERT: A 243 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 46 ASP cc_start: 0.7341 (m-30) cc_final: 0.7095 (m-30) REVERT: B 47 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: B 65 GLN cc_start: 0.8673 (mt0) cc_final: 0.8453 (mt0) REVERT: B 67 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: B 121 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7697 (tttt) REVERT: C 118 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8337 (mp) REVERT: C 145 SER cc_start: 0.7966 (m) cc_final: 0.7760 (p) REVERT: C 168 MET cc_start: 0.8285 (mmp) cc_final: 0.8018 (tpt) REVERT: C 210 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: C 261 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7605 (mtp85) REVERT: C 310 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8414 (mtpt) REVERT: E 168 MET cc_start: 0.8328 (mmt) cc_final: 0.7952 (tpt) REVERT: E 223 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8614 (t) REVERT: D 17 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8155 (ttp) REVERT: F 17 MET cc_start: 0.8521 (tpp) cc_final: 0.8294 (ttm) REVERT: F 105 GLN cc_start: 0.8759 (tp40) cc_final: 0.8494 (tp-100) REVERT: F 146 ASN cc_start: 0.7482 (m110) cc_final: 0.6988 (m110) REVERT: F 151 SER cc_start: 0.8015 (t) cc_final: 0.7299 (p) outliers start: 68 outliers final: 32 residues processed: 216 average time/residue: 1.0390 time to fit residues: 246.6384 Evaluate side-chains 188 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 30 GLU 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: 1.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS E 18 HIS E 312 ASN D 34 GLN D 47 GLN D 105 GLN F 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 1.0141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12234 Z= 0.305 Angle : 0.613 10.171 16590 Z= 0.318 Chirality : 0.047 0.275 1920 Planarity : 0.005 0.053 2127 Dihedral : 8.116 68.305 2259 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.40 % Allowed : 21.94 % Favored : 71.66 % 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: -0.92 (0.20), residues: 1458 helix: 1.54 (0.28), residues: 357 sheet: 0.25 (0.33), residues: 234 loop : -1.92 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.002 HIS A 75 PHE 0.018 0.002 PHE B 24 TYR 0.017 0.002 TYR D 162 ARG 0.005 0.001 ARG C 201 *********************** 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 239 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 157 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8045 (tpt) REVERT: A 243 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 34 GLN cc_start: 0.8419 (tt0) cc_final: 0.8102 (tt0) REVERT: B 46 ASP cc_start: 0.7393 (m-30) cc_final: 0.7149 (m-30) REVERT: B 47 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: B 65 GLN cc_start: 0.8641 (mt0) cc_final: 0.8435 (mt0) REVERT: B 67 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: B 121 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7667 (tttt) REVERT: C 119 GLU cc_start: 0.8444 (tt0) cc_final: 0.8161 (tt0) REVERT: C 168 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8089 (tpt) REVERT: C 210 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: C 245 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8076 (mt) REVERT: C 261 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7451 (mtp85) REVERT: C 275 ASP cc_start: 0.7286 (m-30) cc_final: 0.6897 (m-30) REVERT: C 310 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8374 (mtpt) REVERT: E 51 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7424 (mt) REVERT: E 62 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8050 (mp) REVERT: E 168 MET cc_start: 0.8334 (mmt) cc_final: 0.8016 (tpt) REVERT: E 223 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8509 (t) REVERT: E 261 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7233 (mmm-85) REVERT: E 276 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7713 (p) REVERT: D 17 MET cc_start: 0.8372 (tpp) cc_final: 0.8164 (ttp) REVERT: D 128 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: F 47 GLN cc_start: 0.7763 (mt0) cc_final: 0.7555 (mt0) REVERT: F 151 SER cc_start: 0.8208 (t) cc_final: 0.7575 (p) outliers start: 82 outliers final: 40 residues processed: 222 average time/residue: 1.0024 time to fit residues: 245.4353 Evaluate side-chains 202 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 147 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE 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: 0.0070 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS C 246 ASN E 18 HIS E 33 GLN E 312 ASN D 34 GLN D 47 GLN D 146 ASN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 1.0286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12234 Z= 0.207 Angle : 0.551 9.877 16590 Z= 0.286 Chirality : 0.045 0.249 1920 Planarity : 0.004 0.040 2127 Dihedral : 7.450 62.245 2259 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.15 % Allowed : 23.42 % Favored : 71.43 % 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: -0.63 (0.20), residues: 1458 helix: 1.84 (0.28), residues: 357 sheet: -0.04 (0.31), residues: 264 loop : -1.66 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 PHE 0.013 0.002 PHE F 24 TYR 0.013 0.001 TYR D 162 ARG 0.006 0.000 ARG C 201 *********************** 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 216 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 150 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: B 34 GLN cc_start: 0.8450 (tt0) cc_final: 0.8171 (tt0) REVERT: B 46 ASP cc_start: 0.7369 (m-30) cc_final: 0.7127 (m-30) REVERT: B 47 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: B 65 GLN cc_start: 0.8642 (mt0) cc_final: 0.8425 (mt0) REVERT: B 67 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: B 121 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7663 (tttt) REVERT: C 118 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 119 GLU cc_start: 0.8374 (tt0) cc_final: 0.8113 (tt0) REVERT: C 168 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8131 (tpt) REVERT: C 214 ILE cc_start: 0.8665 (tt) cc_final: 0.8453 (mt) REVERT: C 245 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8094 (mt) REVERT: C 261 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7333 (mtp85) REVERT: C 275 ASP cc_start: 0.7266 (m-30) cc_final: 0.6964 (m-30) REVERT: E 62 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8116 (mp) REVERT: E 168 MET cc_start: 0.8304 (mmt) cc_final: 0.8054 (tpt) REVERT: E 195 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: E 201 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (ptt90) REVERT: E 223 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8494 (t) REVERT: E 276 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7813 (p) REVERT: F 47 GLN cc_start: 0.7724 (mt0) cc_final: 0.7415 (mt0) REVERT: F 151 SER cc_start: 0.8219 (t) cc_final: 0.7558 (p) outliers start: 66 outliers final: 27 residues processed: 198 average time/residue: 1.1002 time to fit residues: 238.8833 Evaluate side-chains 180 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS E 18 HIS E 33 GLN D 34 GLN D 47 GLN F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 1.0417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12234 Z= 0.278 Angle : 0.594 11.242 16590 Z= 0.308 Chirality : 0.046 0.261 1920 Planarity : 0.005 0.042 2127 Dihedral : 7.431 61.629 2259 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.15 % Allowed : 23.34 % Favored : 71.51 % 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: -0.65 (0.20), residues: 1458 helix: 1.88 (0.28), residues: 357 sheet: 0.23 (0.33), residues: 234 loop : -1.74 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.017 0.002 HIS C 18 PHE 0.017 0.002 PHE F 24 TYR 0.014 0.002 TYR A 308 ARG 0.005 0.000 ARG C 201 *********************** 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 214 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 148 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8415 (pt) cc_final: 0.7728 (tt) REVERT: A 35 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: B 34 GLN cc_start: 0.8483 (tt0) cc_final: 0.8196 (tt0) REVERT: B 46 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: B 47 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: B 65 GLN cc_start: 0.8669 (mt0) cc_final: 0.8435 (mt0) REVERT: B 67 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: B 121 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7686 (tttt) REVERT: B 125 GLN cc_start: 0.7760 (tt0) cc_final: 0.7479 (mt0) REVERT: C 119 GLU cc_start: 0.8370 (tt0) cc_final: 0.8073 (tt0) REVERT: C 168 MET cc_start: 0.8387 (mmp) cc_final: 0.8166 (tpt) REVERT: C 210 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: C 214 ILE cc_start: 0.8681 (tt) cc_final: 0.8465 (mt) REVERT: C 245 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8094 (mt) REVERT: C 261 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: C 310 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8404 (mtpt) REVERT: E 62 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8213 (mp) REVERT: E 168 MET cc_start: 0.8320 (mmt) cc_final: 0.8086 (tpt) REVERT: E 195 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: E 201 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8032 (ptt90) REVERT: E 223 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8515 (t) REVERT: E 261 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7292 (mmm-85) REVERT: D 128 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: F 47 GLN cc_start: 0.7748 (mt0) cc_final: 0.7457 (mt0) REVERT: F 151 SER cc_start: 0.8299 (t) cc_final: 0.7674 (p) outliers start: 66 outliers final: 34 residues processed: 197 average time/residue: 1.0282 time to fit residues: 222.9093 Evaluate side-chains 194 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 146 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 33 GLN D 34 GLN D 47 GLN D 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 1.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12234 Z= 0.237 Angle : 0.561 10.051 16590 Z= 0.291 Chirality : 0.045 0.246 1920 Planarity : 0.004 0.039 2127 Dihedral : 7.083 57.723 2259 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.07 % Allowed : 23.26 % Favored : 71.66 % 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: -0.53 (0.21), residues: 1458 helix: 1.97 (0.28), residues: 360 sheet: 0.28 (0.33), residues: 234 loop : -1.65 (0.17), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 PHE 0.013 0.002 PHE D 9 TYR 0.013 0.002 TYR D 162 ARG 0.005 0.000 ARG C 201 *********************** 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 211 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 146 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8485 (pt) cc_final: 0.7856 (tt) REVERT: A 35 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: B 34 GLN cc_start: 0.8452 (tt0) cc_final: 0.8166 (tt0) REVERT: B 46 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: B 65 GLN cc_start: 0.8667 (mt0) cc_final: 0.8458 (mt0) REVERT: B 67 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: B 121 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7689 (tttt) REVERT: B 125 GLN cc_start: 0.7737 (tt0) cc_final: 0.7475 (mt0) REVERT: C 118 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8343 (mp) REVERT: C 119 GLU cc_start: 0.8338 (tt0) cc_final: 0.8071 (tt0) REVERT: C 168 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (tpt) REVERT: C 245 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8126 (mt) REVERT: E 62 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 168 MET cc_start: 0.8312 (mmt) cc_final: 0.8075 (tpt) REVERT: E 195 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: E 223 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8507 (t) REVERT: F 47 GLN cc_start: 0.7754 (mt0) cc_final: 0.7433 (mt0) REVERT: F 151 SER cc_start: 0.8337 (t) cc_final: 0.7758 (p) outliers start: 65 outliers final: 35 residues processed: 197 average time/residue: 1.0868 time to fit residues: 234.4909 Evaluate side-chains 181 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN C 18 HIS E 18 HIS E 33 GLN D 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 1.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12234 Z= 0.297 Angle : 0.613 10.835 16590 Z= 0.316 Chirality : 0.047 0.257 1920 Planarity : 0.005 0.042 2127 Dihedral : 7.159 57.328 2259 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.84 % Allowed : 23.65 % Favored : 71.51 % 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: -0.59 (0.20), residues: 1458 helix: 1.92 (0.28), residues: 360 sheet: 0.23 (0.33), residues: 234 loop : -1.69 (0.17), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS E 75 PHE 0.018 0.002 PHE F 24 TYR 0.014 0.002 TYR C 308 ARG 0.005 0.000 ARG C 201 *********************** 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 210 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 148 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.7884 (tt) REVERT: A 35 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: B 34 GLN cc_start: 0.8464 (tt0) cc_final: 0.8183 (tt0) REVERT: B 67 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: B 121 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7703 (tttt) REVERT: B 125 GLN cc_start: 0.7877 (tt0) cc_final: 0.7590 (mt0) REVERT: C 119 GLU cc_start: 0.8341 (tt0) cc_final: 0.8062 (tt0) REVERT: C 168 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8227 (tpt) REVERT: C 245 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8106 (mt) REVERT: E 62 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8288 (mp) REVERT: E 168 MET cc_start: 0.8350 (mmt) cc_final: 0.8140 (tpt) REVERT: E 201 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8059 (ptt90) REVERT: E 223 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8526 (t) REVERT: D 128 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6771 (tp30) REVERT: F 47 GLN cc_start: 0.7880 (mt0) cc_final: 0.7556 (mt0) REVERT: F 151 SER cc_start: 0.8374 (t) cc_final: 0.7843 (p) outliers start: 62 outliers final: 38 residues processed: 197 average time/residue: 1.1170 time to fit residues: 240.8982 Evaluate side-chains 188 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 141 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 47 GLN B 125 GLN C 18 HIS E 18 HIS E 33 GLN D 34 GLN D 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 1.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12234 Z= 0.254 Angle : 0.582 10.282 16590 Z= 0.301 Chirality : 0.046 0.272 1920 Planarity : 0.005 0.048 2127 Dihedral : 7.002 55.302 2259 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.90 % Allowed : 24.90 % Favored : 71.19 % 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: -0.50 (0.21), residues: 1458 helix: 2.04 (0.28), residues: 357 sheet: 0.27 (0.33), residues: 234 loop : -1.64 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 PHE 0.014 0.002 PHE F 24 TYR 0.012 0.002 TYR D 162 ARG 0.005 0.000 ARG C 201 ********************** 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 188 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.7900 (tt) REVERT: A 35 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 34 GLN cc_start: 0.8457 (tt0) cc_final: 0.8185 (tt0) REVERT: B 67 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: B 121 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7684 (tttt) REVERT: B 125 GLN cc_start: 0.7774 (tt0) cc_final: 0.7524 (mt0) REVERT: C 119 GLU cc_start: 0.8330 (tt0) cc_final: 0.8082 (tt0) REVERT: C 245 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8101 (mt) REVERT: E 62 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8274 (mp) REVERT: E 168 MET cc_start: 0.8337 (mmt) cc_final: 0.8125 (tpt) REVERT: E 201 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8043 (ptt90) REVERT: E 223 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8512 (t) REVERT: F 47 GLN cc_start: 0.7827 (mt0) cc_final: 0.7513 (mt0) REVERT: F 65 GLN cc_start: 0.8784 (mt0) cc_final: 0.8449 (mt0) REVERT: F 151 SER cc_start: 0.8343 (t) cc_final: 0.7844 (p) outliers start: 50 outliers final: 38 residues processed: 179 average time/residue: 1.1545 time to fit residues: 225.4293 Evaluate side-chains 183 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN C 18 HIS E 33 GLN D 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.125406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.104218 restraints weight = 13729.446| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.80 r_work: 0.2937 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 1.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12234 Z= 0.252 Angle : 0.581 10.168 16590 Z= 0.300 Chirality : 0.046 0.243 1920 Planarity : 0.005 0.045 2127 Dihedral : 6.948 54.813 2259 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.22 % Allowed : 24.59 % Favored : 71.19 % 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: -0.48 (0.21), residues: 1458 helix: 2.07 (0.28), residues: 357 sheet: 0.26 (0.33), residues: 234 loop : -1.63 (0.18), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 PHE 0.015 0.002 PHE F 24 TYR 0.012 0.002 TYR A 308 ARG 0.005 0.000 ARG C 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4580.81 seconds wall clock time: 82 minutes 10.00 seconds (4930.00 seconds total)