Starting phenix.real_space_refine on Mon Mar 11 09:44:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn8_34157/03_2024/8gn8_34157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn8_34157/03_2024/8gn8_34157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn8_34157/03_2024/8gn8_34157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn8_34157/03_2024/8gn8_34157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn8_34157/03_2024/8gn8_34157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn8_34157/03_2024/8gn8_34157.pdb" } resolution = 3.5 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= 0.006 sd= 0.116 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 70 5.16 5 C 5230 2.51 5 N 1340 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7920 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Time building chain proxies: 4.33, per 1000 atoms: 0.55 Number of scatterers: 7920 At special positions: 0 Unit cell: (90.16, 90.16, 95.68, 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 70 16.00 O 1280 8.00 N 1340 7.00 C 5230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 175 " 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 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 70.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 35 through 42 removed outlier: 3.959A pdb=" N ARG D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.408A pdb=" N ASP D 47 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 48 " --> pdb=" O TYR D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 102 removed outlier: 3.713A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 3.867A pdb=" N SER D 93 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.198A pdb=" N LEU D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 140 through 166 removed outlier: 3.728A pdb=" N ILE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 219 removed outlier: 3.657A pdb=" N LYS D 194 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.691A pdb=" N ARG D 227 " --> pdb=" O MET D 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.423A pdb=" N ASP A 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 48 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.724A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.835A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.739A pdb=" N ILE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 225 removed outlier: 3.648A pdb=" N LYS A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 43 through 47 removed outlier: 4.389A pdb=" N ASP B 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 102 removed outlier: 3.718A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.892A pdb=" N SER B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.214A pdb=" N LEU B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 107' Processing helix chain 'B' and resid 140 through 166 removed outlier: 3.730A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 225 removed outlier: 3.647A pdb=" N LYS B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.967A pdb=" N ARG C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.411A pdb=" N ASP C 47 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 102 removed outlier: 3.711A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.898A pdb=" N SER C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 4.198A pdb=" N LEU C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 107' Processing helix chain 'C' and resid 140 through 166 removed outlier: 3.761A pdb=" N ILE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 225 removed outlier: 3.649A pdb=" N LYS C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 16 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 35 through 42 removed outlier: 3.943A pdb=" N ARG E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 4.404A pdb=" N ASP E 47 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 107 removed outlier: 3.713A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.991A pdb=" N SER E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 166 removed outlier: 3.725A pdb=" N ILE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 225 removed outlier: 3.650A pdb=" N LYS E 194 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 216 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 221 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 172 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.889A pdb=" N VAL A 53 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.854A pdb=" N VAL B 53 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.860A pdb=" N VAL E 53 " --> pdb=" O TYR E 187 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1278 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: 1.94 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2450 1.35 - 1.46: 1954 1.46 - 1.58: 3621 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 8120 Sorted by residual: bond pdb=" CA PHE D 9 " pdb=" C PHE D 9 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.41e+00 bond pdb=" CA PHE E 9 " pdb=" C PHE E 9 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.35e+00 bond pdb=" CA PHE A 9 " pdb=" C PHE A 9 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.28e+00 bond pdb=" CA PHE C 9 " pdb=" C PHE C 9 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.24e+00 bond pdb=" CA PHE B 9 " pdb=" C PHE B 9 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.34e-02 5.57e+03 9.51e-01 ... (remaining 8115 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 336 107.34 - 114.00: 4572 114.00 - 120.67: 3424 120.67 - 127.33: 2628 127.33 - 133.99: 90 Bond angle restraints: 11050 Sorted by residual: angle pdb=" N GLY A 8 " pdb=" CA GLY A 8 " pdb=" C GLY A 8 " ideal model delta sigma weight residual 110.21 107.14 3.07 9.10e-01 1.21e+00 1.13e+01 angle pdb=" N GLY B 8 " pdb=" CA GLY B 8 " pdb=" C GLY B 8 " ideal model delta sigma weight residual 110.21 107.16 3.05 9.10e-01 1.21e+00 1.12e+01 angle pdb=" C PHE B 9 " pdb=" CA PHE B 9 " pdb=" CB PHE B 9 " ideal model delta sigma weight residual 110.42 116.63 -6.21 1.99e+00 2.53e-01 9.74e+00 angle pdb=" C PHE E 9 " pdb=" CA PHE E 9 " pdb=" CB PHE E 9 " ideal model delta sigma weight residual 110.42 116.55 -6.13 1.99e+00 2.53e-01 9.49e+00 angle pdb=" C PHE A 9 " pdb=" CA PHE A 9 " pdb=" CB PHE A 9 " ideal model delta sigma weight residual 110.42 116.42 -6.00 1.99e+00 2.53e-01 9.09e+00 ... (remaining 11045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 3806 11.82 - 23.65: 530 23.65 - 35.47: 313 35.47 - 47.29: 124 47.29 - 59.12: 52 Dihedral angle restraints: 4825 sinusoidal: 1915 harmonic: 2910 Sorted by residual: dihedral pdb=" CA PRO D 178 " pdb=" C PRO D 178 " pdb=" N PRO D 179 " pdb=" CA PRO D 179 " ideal model delta harmonic sigma weight residual 180.00 133.93 46.07 0 5.00e+00 4.00e-02 8.49e+01 dihedral pdb=" CA PRO E 178 " pdb=" C PRO E 178 " pdb=" N PRO E 179 " pdb=" CA PRO E 179 " ideal model delta harmonic sigma weight residual 180.00 133.94 46.06 0 5.00e+00 4.00e-02 8.49e+01 dihedral pdb=" CA PRO A 178 " pdb=" C PRO A 178 " pdb=" N PRO A 179 " pdb=" CA PRO A 179 " ideal model delta harmonic sigma weight residual 180.00 134.14 45.86 0 5.00e+00 4.00e-02 8.41e+01 ... (remaining 4822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 676 0.024 - 0.048: 311 0.048 - 0.072: 223 0.072 - 0.096: 74 0.096 - 0.120: 26 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA VAL E 183 " pdb=" N VAL E 183 " pdb=" C VAL E 183 " pdb=" CB VAL E 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA VAL C 183 " pdb=" N VAL C 183 " pdb=" C VAL C 183 " pdb=" CB VAL C 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1307 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 9 " 0.021 2.00e-02 2.50e+03 2.82e-02 1.40e+01 pdb=" CG PHE B 9 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE B 9 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 9 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 9 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 9 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 9 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 9 " 0.020 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE E 9 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE E 9 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE E 9 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E 9 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 9 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 9 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO C 179 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.041 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1853 2.80 - 3.32: 6851 3.32 - 3.85: 12089 3.85 - 4.37: 12711 4.37 - 4.90: 23595 Nonbonded interactions: 57099 Sorted by model distance: nonbonded pdb=" O SER A 70 " pdb=" OG SER A 70 " model vdw 2.271 2.440 nonbonded pdb=" O SER B 70 " pdb=" OG SER B 70 " model vdw 2.272 2.440 nonbonded pdb=" O SER C 70 " pdb=" OG SER C 70 " model vdw 2.272 2.440 nonbonded pdb=" O SER D 70 " pdb=" OG SER D 70 " model vdw 2.275 2.440 nonbonded pdb=" O SER E 70 " pdb=" OG SER E 70 " model vdw 2.275 2.440 ... (remaining 57094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.910 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: 3.880 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.003 0.029 8120 Z= 0.160 Angle : 0.658 9.866 11050 Z= 0.359 Chirality : 0.039 0.120 1310 Planarity : 0.006 0.074 1360 Dihedral : 16.612 58.699 2900 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.34 % Allowed : 31.61 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 0.26 (0.30), residues: 990 helix: 1.09 (0.23), residues: 645 sheet: 1.60 (0.79), residues: 50 loop : -2.18 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 202 HIS 0.003 0.001 HIS A 74 PHE 0.065 0.002 PHE B 9 TYR 0.005 0.001 TYR C 162 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.759 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.1410 time to fit residues: 18.4606 Evaluate side-chains 79 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 9.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8120 Z= 0.152 Angle : 0.567 8.116 11050 Z= 0.281 Chirality : 0.037 0.119 1310 Planarity : 0.005 0.069 1360 Dihedral : 4.835 45.060 1103 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.56 % Allowed : 29.54 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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 (0.30), residues: 990 helix: 1.39 (0.23), residues: 650 sheet: 1.77 (0.75), residues: 50 loop : -2.43 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.003 0.001 HIS C 74 PHE 0.015 0.001 PHE D 9 TYR 0.011 0.001 TYR D 162 ARG 0.003 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.896 Fit side-chains REVERT: B 6 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7105 (tt) outliers start: 31 outliers final: 22 residues processed: 104 average time/residue: 0.1328 time to fit residues: 21.4987 Evaluate side-chains 103 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8120 Z= 0.159 Angle : 0.553 8.732 11050 Z= 0.273 Chirality : 0.038 0.118 1310 Planarity : 0.005 0.066 1360 Dihedral : 4.720 45.404 1100 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.71 % Allowed : 29.77 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 990 helix: 1.47 (0.23), residues: 660 sheet: 2.09 (0.72), residues: 50 loop : -2.19 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.004 0.001 HIS C 74 PHE 0.040 0.001 PHE E 9 TYR 0.011 0.001 TYR D 162 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 83 time to evaluate : 0.806 Fit side-chains REVERT: B 6 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7046 (tt) outliers start: 41 outliers final: 26 residues processed: 110 average time/residue: 0.1685 time to fit residues: 26.3455 Evaluate side-chains 108 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 chunk 54 optimal weight: 9.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8120 Z= 0.157 Angle : 0.544 8.682 11050 Z= 0.269 Chirality : 0.038 0.119 1310 Planarity : 0.005 0.066 1360 Dihedral : 4.645 44.949 1100 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.86 % Allowed : 28.28 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 0.97 (0.30), residues: 990 helix: 1.58 (0.22), residues: 665 sheet: 2.12 (0.71), residues: 50 loop : -2.09 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.003 0.001 HIS C 74 PHE 0.041 0.001 PHE E 9 TYR 0.010 0.001 TYR D 162 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 80 time to evaluate : 0.930 Fit side-chains REVERT: A 146 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7657 (t-90) REVERT: B 6 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7054 (tt) REVERT: C 198 MET cc_start: 0.7969 (ttm) cc_final: 0.7672 (ttm) outliers start: 51 outliers final: 41 residues processed: 110 average time/residue: 0.1297 time to fit residues: 22.2371 Evaluate side-chains 120 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 77 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8120 Z= 0.157 Angle : 0.546 9.176 11050 Z= 0.269 Chirality : 0.038 0.119 1310 Planarity : 0.005 0.064 1360 Dihedral : 4.642 44.961 1100 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 7.59 % Allowed : 26.78 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.14 (0.30), residues: 990 helix: 1.69 (0.22), residues: 665 sheet: 2.00 (0.71), residues: 50 loop : -1.90 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.003 0.001 HIS E 74 PHE 0.046 0.001 PHE E 9 TYR 0.008 0.001 TYR D 162 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 78 time to evaluate : 0.898 Fit side-chains REVERT: A 146 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7552 (t-90) REVERT: B 6 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7071 (tt) REVERT: B 74 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6242 (p-80) REVERT: B 190 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7540 (ptp-170) outliers start: 66 outliers final: 43 residues processed: 120 average time/residue: 0.1564 time to fit residues: 27.7110 Evaluate side-chains 122 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 75 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.0370 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8120 Z= 0.131 Angle : 0.531 8.738 11050 Z= 0.263 Chirality : 0.037 0.119 1310 Planarity : 0.005 0.062 1360 Dihedral : 4.473 43.536 1100 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.90 % Allowed : 26.55 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.44 (0.30), residues: 990 helix: 1.92 (0.22), residues: 665 sheet: 1.98 (0.71), residues: 50 loop : -1.76 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 202 HIS 0.002 0.000 HIS B 74 PHE 0.046 0.001 PHE E 9 TYR 0.010 0.001 TYR D 162 ARG 0.003 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 87 time to evaluate : 0.914 Fit side-chains REVERT: D 171 LYS cc_start: 0.8328 (tppt) cc_final: 0.8027 (mttp) REVERT: D 217 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 190 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7762 (ptp-170) REVERT: B 6 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7056 (tt) REVERT: B 74 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6126 (p-80) REVERT: B 190 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7466 (ptp-170) REVERT: E 190 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7932 (ptt180) outliers start: 60 outliers final: 37 residues processed: 125 average time/residue: 0.1951 time to fit residues: 34.1446 Evaluate side-chains 122 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 79 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8120 Z= 0.147 Angle : 0.546 9.394 11050 Z= 0.268 Chirality : 0.038 0.119 1310 Planarity : 0.005 0.062 1360 Dihedral : 4.492 43.719 1100 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.98 % Allowed : 26.78 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.49 (0.30), residues: 990 helix: 1.97 (0.22), residues: 665 sheet: 1.86 (0.70), residues: 50 loop : -1.73 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.003 0.001 HIS B 74 PHE 0.050 0.001 PHE E 9 TYR 0.007 0.001 TYR D 162 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 78 time to evaluate : 0.862 Fit side-chains REVERT: D 171 LYS cc_start: 0.8312 (tppt) cc_final: 0.8027 (mttp) REVERT: D 217 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 190 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7787 (ptp-170) REVERT: B 6 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7095 (tt) REVERT: B 74 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6298 (p-80) REVERT: E 190 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7977 (ptt180) outliers start: 52 outliers final: 38 residues processed: 113 average time/residue: 0.1673 time to fit residues: 27.5589 Evaluate side-chains 121 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 78 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8120 Z= 0.166 Angle : 0.560 9.694 11050 Z= 0.275 Chirality : 0.038 0.118 1310 Planarity : 0.005 0.061 1360 Dihedral : 4.568 44.263 1100 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.55 % Allowed : 26.09 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.52 (0.30), residues: 990 helix: 2.25 (0.22), residues: 645 sheet: 1.65 (0.69), residues: 50 loop : -2.11 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 202 HIS 0.003 0.001 HIS B 74 PHE 0.051 0.001 PHE E 9 TYR 0.006 0.001 TYR D 162 ARG 0.002 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 80 time to evaluate : 0.795 Fit side-chains REVERT: A 190 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7856 (ptp-170) REVERT: B 6 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7023 (tt) REVERT: B 74 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6341 (p-80) REVERT: B 190 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7578 (ptp-170) REVERT: E 190 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8037 (ptt180) outliers start: 57 outliers final: 44 residues processed: 118 average time/residue: 0.1519 time to fit residues: 26.0845 Evaluate side-chains 128 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 79 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 57 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: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8120 Z= 0.151 Angle : 0.554 9.643 11050 Z= 0.273 Chirality : 0.038 0.122 1310 Planarity : 0.005 0.060 1360 Dihedral : 4.549 43.583 1100 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.21 % Allowed : 26.32 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.64 (0.30), residues: 990 helix: 2.37 (0.22), residues: 645 sheet: 1.56 (0.68), residues: 50 loop : -2.12 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 202 HIS 0.003 0.001 HIS E 74 PHE 0.054 0.001 PHE E 9 TYR 0.007 0.001 TYR D 162 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 81 time to evaluate : 0.813 Fit side-chains REVERT: A 190 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7836 (ptp-170) REVERT: B 6 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7096 (tt) REVERT: B 74 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6304 (p-80) REVERT: B 190 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7536 (ptp-170) REVERT: C 30 MET cc_start: 0.8612 (tpp) cc_final: 0.8308 (mmp) REVERT: E 190 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8059 (ptt180) outliers start: 54 outliers final: 47 residues processed: 113 average time/residue: 0.1639 time to fit residues: 26.8035 Evaluate side-chains 132 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 80 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8120 Z= 0.152 Angle : 0.558 9.581 11050 Z= 0.273 Chirality : 0.038 0.126 1310 Planarity : 0.005 0.060 1360 Dihedral : 4.528 43.681 1100 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.32 % Allowed : 26.32 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.68 (0.30), residues: 990 helix: 2.17 (0.22), residues: 670 sheet: 1.49 (0.67), residues: 50 loop : -1.81 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.003 0.001 HIS B 74 PHE 0.054 0.001 PHE E 9 TYR 0.006 0.001 TYR D 162 ARG 0.001 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 81 time to evaluate : 0.858 Fit side-chains REVERT: A 190 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7832 (ptp-170) REVERT: B 6 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7106 (tt) REVERT: B 74 HIS cc_start: 0.6794 (OUTLIER) cc_final: 0.6346 (p-80) REVERT: B 190 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7527 (ptp-170) REVERT: C 30 MET cc_start: 0.8643 (tpp) cc_final: 0.8358 (mmp) REVERT: E 190 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8037 (ptt180) outliers start: 55 outliers final: 45 residues processed: 114 average time/residue: 0.1694 time to fit residues: 28.3044 Evaluate side-chains 129 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 79 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.095997 restraints weight = 9719.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098874 restraints weight = 5739.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100645 restraints weight = 4258.288| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8120 Z= 0.170 Angle : 0.567 9.989 11050 Z= 0.278 Chirality : 0.038 0.124 1310 Planarity : 0.005 0.061 1360 Dihedral : 4.576 44.181 1100 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.75 % Allowed : 26.90 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 1.64 (0.30), residues: 990 helix: 2.13 (0.22), residues: 670 sheet: 1.36 (0.67), residues: 50 loop : -1.79 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 202 HIS 0.003 0.001 HIS B 74 PHE 0.055 0.001 PHE E 9 TYR 0.006 0.001 TYR D 162 ARG 0.001 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.71 seconds wall clock time: 28 minutes 3.80 seconds (1683.80 seconds total)