Starting phenix.real_space_refine on Sat Mar 16 18:43:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwn_20508/03_2024/6pwn_20508_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwn_20508/03_2024/6pwn_20508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwn_20508/03_2024/6pwn_20508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwn_20508/03_2024/6pwn_20508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwn_20508/03_2024/6pwn_20508_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwn_20508/03_2024/6pwn_20508_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 49 5.16 5 C 9954 2.51 5 N 2597 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A ASP 8": "OD1" <-> "OD2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ASP 8": "OD1" <-> "OD2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C ASP 8": "OD1" <-> "OD2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D ASP 8": "OD1" <-> "OD2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 2": "OE1" <-> "OE2" Residue "F ASP 8": "OD1" <-> "OD2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2": "OE1" <-> "OE2" Residue "G ASP 8": "OD1" <-> "OD2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15379 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'POV': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'POV': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.32, per 1000 atoms: 0.54 Number of scatterers: 15379 At special positions: 0 Unit cell: (101.08, 101.08, 147.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 7 15.00 O 2772 8.00 N 2597 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.91 Conformation dependent library (CDL) restraints added in 3.0 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 50.0% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 21 through 57 Processing helix chain 'A' and resid 63 through 89 Processing helix chain 'A' and resid 94 through 127 removed outlier: 4.887A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 246 through 264 removed outlier: 3.630A pdb=" N ASP A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 21 through 57 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 94 through 127 removed outlier: 4.886A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 246 through 264 removed outlier: 3.630A pdb=" N ASP B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 21 through 57 Processing helix chain 'C' and resid 63 through 89 Processing helix chain 'C' and resid 94 through 127 removed outlier: 4.886A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 170 No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 246 through 264 removed outlier: 3.630A pdb=" N ASP C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 21 through 57 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 94 through 127 removed outlier: 4.887A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 246 through 264 removed outlier: 3.630A pdb=" N ASP D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 21 through 57 Processing helix chain 'E' and resid 63 through 89 Processing helix chain 'E' and resid 94 through 127 removed outlier: 4.887A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 116 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 No H-bonds generated for 'chain 'E' and resid 167 through 170' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 246 through 264 removed outlier: 3.630A pdb=" N ASP E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 21 through 57 Processing helix chain 'F' and resid 63 through 89 Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.887A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER F 116 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 246 through 264 removed outlier: 3.629A pdb=" N ASP F 262 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 21 through 57 Processing helix chain 'G' and resid 63 through 89 Processing helix chain 'G' and resid 94 through 127 removed outlier: 4.887A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 170 No H-bonds generated for 'chain 'G' and resid 167 through 170' Processing helix chain 'G' and resid 198 through 211 Processing helix chain 'G' and resid 246 through 264 removed outlier: 3.630A pdb=" N ASP G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.777A pdb=" N VAL A 136 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL A 239 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.777A pdb=" N VAL B 136 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL B 239 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.776A pdb=" N VAL C 136 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL C 239 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.777A pdb=" N VAL D 136 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 183 through 192 removed outlier: 3.719A pdb=" N VAL D 239 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.777A pdb=" N VAL E 136 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL E 239 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.777A pdb=" N VAL F 136 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 183 through 192 removed outlier: 3.719A pdb=" N VAL F 239 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 175 through 177 removed outlier: 3.777A pdb=" N VAL G 136 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 183 through 192 removed outlier: 3.719A pdb=" N VAL G 239 " --> pdb=" O ASN G 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2499 1.31 - 1.43: 3658 1.43 - 1.56: 9124 1.56 - 1.68: 168 1.68 - 1.80: 105 Bond restraints: 15554 Sorted by residual: bond pdb=" C31 POV F 301 " pdb=" O31 POV F 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C31 POV E 301 " pdb=" O31 POV E 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C31 POV B 301 " pdb=" O31 POV B 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 15549 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 241 107.14 - 113.85: 9357 113.85 - 120.56: 6092 120.56 - 127.27: 5226 127.27 - 133.98: 77 Bond angle restraints: 20993 Sorted by residual: angle pdb=" O13 POV B 301 " pdb=" P POV B 301 " pdb=" O14 POV B 301 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 POV F 301 " pdb=" P POV F 301 " pdb=" O14 POV F 301 " ideal model delta sigma weight residual 121.11 109.53 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 POV G 301 " pdb=" P POV G 301 " pdb=" O14 POV G 301 " ideal model delta sigma weight residual 121.11 109.53 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O11 POV F 301 " pdb=" P POV F 301 " pdb=" O12 POV F 301 " ideal model delta sigma weight residual 97.67 109.24 -11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 POV D 301 " pdb=" P POV D 301 " pdb=" O14 POV D 301 " ideal model delta sigma weight residual 121.11 109.55 11.56 3.00e+00 1.11e-01 1.49e+01 ... (remaining 20988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 8329 16.00 - 32.00: 840 32.00 - 48.00: 183 48.00 - 64.00: 56 64.00 - 80.00: 35 Dihedral angle restraints: 9443 sinusoidal: 3836 harmonic: 5607 Sorted by residual: dihedral pdb=" CA ASP D 8 " pdb=" CB ASP D 8 " pdb=" CG ASP D 8 " pdb=" OD1 ASP D 8 " ideal model delta sinusoidal sigma weight residual -30.00 -88.70 58.70 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP F 8 " pdb=" CB ASP F 8 " pdb=" CG ASP F 8 " pdb=" OD1 ASP F 8 " ideal model delta sinusoidal sigma weight residual -30.00 -88.70 58.70 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP E 8 " pdb=" CB ASP E 8 " pdb=" CG ASP E 8 " pdb=" OD1 ASP E 8 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 9440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1246 0.027 - 0.054: 788 0.054 - 0.081: 251 0.081 - 0.108: 171 0.108 - 0.135: 64 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CB ILE A 165 " pdb=" CA ILE A 165 " pdb=" CG1 ILE A 165 " pdb=" CG2 ILE A 165 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CB ILE E 165 " pdb=" CA ILE E 165 " pdb=" CG1 ILE E 165 " pdb=" CG2 ILE E 165 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CB ILE D 165 " pdb=" CA ILE D 165 " pdb=" CG1 ILE D 165 " pdb=" CG2 ILE D 165 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2517 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER G 9 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C SER G 9 " 0.030 2.00e-02 2.50e+03 pdb=" O SER G 9 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE G 10 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 9 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C SER B 9 " -0.030 2.00e-02 2.50e+03 pdb=" O SER B 9 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE B 10 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 9 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C SER A 9 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 9 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 10 " 0.010 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3887 2.80 - 3.33: 15607 3.33 - 3.85: 23901 3.85 - 4.38: 28572 4.38 - 4.90: 49234 Nonbonded interactions: 121201 Sorted by model distance: nonbonded pdb=" OE2 GLU A 134 " pdb=" ND2 ASN A 177 " model vdw 2.276 2.520 nonbonded pdb=" OE2 GLU F 134 " pdb=" ND2 ASN F 177 " model vdw 2.276 2.520 nonbonded pdb=" OE2 GLU C 134 " pdb=" ND2 ASN C 177 " model vdw 2.276 2.520 nonbonded pdb=" OE2 GLU G 134 " pdb=" ND2 ASN G 177 " model vdw 2.277 2.520 nonbonded pdb=" OE2 GLU E 134 " pdb=" ND2 ASN E 177 " model vdw 2.277 2.520 ... (remaining 121196 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' and (resid 1 through 280 or resid 301)) selection = (chain 'B' and (resid 1 through 280 or resid 301)) selection = (chain 'C' and (resid 1 through 280 or resid 301)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 280 or resid 301)) selection = (chain 'F' and (resid 1 through 280 or resid 301)) selection = chain 'G' } 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: 1.450 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: 0.020 Extract box with map and model: 4.350 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.240 Find NCS groups from input model: 1.190 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.008 0.103 15554 Z= 0.540 Angle : 0.862 11.592 20993 Z= 0.404 Chirality : 0.044 0.135 2520 Planarity : 0.003 0.019 2625 Dihedral : 14.815 80.003 5831 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.44 % Allowed : 5.29 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.17), residues: 1946 helix: -0.48 (0.15), residues: 1008 sheet: -1.57 (0.31), residues: 273 loop : -2.75 (0.19), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 PHE 0.008 0.001 PHE F 68 TYR 0.008 0.001 TYR B 250 ARG 0.002 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7664 (mtm) cc_final: 0.7425 (mmp) REVERT: A 112 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 112 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8743 (tm-30) REVERT: B 134 GLU cc_start: 0.8154 (tt0) cc_final: 0.7732 (tt0) REVERT: C 10 ILE cc_start: 0.4654 (OUTLIER) cc_final: 0.4299 (tp) REVERT: C 21 GLN cc_start: 0.9047 (pt0) cc_final: 0.8820 (pt0) REVERT: C 112 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 220 GLU cc_start: 0.8153 (pp20) cc_final: 0.7866 (pp20) REVERT: D 92 GLN cc_start: 0.8917 (mm110) cc_final: 0.8102 (tt0) REVERT: D 112 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8792 (tm-30) REVERT: D 220 GLU cc_start: 0.8179 (pp20) cc_final: 0.7915 (pp20) REVERT: E 75 TYR cc_start: 0.8258 (m-10) cc_final: 0.8038 (m-80) REVERT: E 92 GLN cc_start: 0.8910 (mm110) cc_final: 0.8121 (tt0) REVERT: E 112 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8890 (tm-30) REVERT: E 220 GLU cc_start: 0.8184 (pp20) cc_final: 0.7844 (pp20) REVERT: F 112 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8805 (tm-30) REVERT: F 134 GLU cc_start: 0.8152 (tt0) cc_final: 0.7911 (tt0) REVERT: F 203 GLN cc_start: 0.8039 (tp40) cc_final: 0.7560 (tm-30) REVERT: F 212 GLU cc_start: 0.7956 (tp30) cc_final: 0.7647 (tp30) REVERT: F 220 GLU cc_start: 0.8204 (pp20) cc_final: 0.7910 (pp20) REVERT: G 21 GLN cc_start: 0.9083 (pt0) cc_final: 0.8869 (pt0) REVERT: G 92 GLN cc_start: 0.8851 (mm110) cc_final: 0.7987 (tt0) REVERT: G 202 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8524 (mtpt) outliers start: 7 outliers final: 0 residues processed: 242 average time/residue: 0.3346 time to fit residues: 111.7160 Evaluate side-chains 187 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15554 Z= 0.168 Angle : 0.494 6.398 20993 Z= 0.256 Chirality : 0.041 0.143 2520 Planarity : 0.003 0.020 2625 Dihedral : 11.887 76.084 2515 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.63 % Allowed : 10.82 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.19), residues: 1946 helix: 1.22 (0.16), residues: 1001 sheet: -0.65 (0.34), residues: 273 loop : -2.27 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 16 PHE 0.007 0.001 PHE C 277 TYR 0.005 0.001 TYR G 27 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.7982 (tp40) cc_final: 0.7769 (tm-30) REVERT: B 92 GLN cc_start: 0.8812 (mm-40) cc_final: 0.7990 (tt0) REVERT: B 134 GLU cc_start: 0.8247 (tt0) cc_final: 0.7726 (tt0) REVERT: B 278 LYS cc_start: 0.8364 (ptmt) cc_final: 0.7801 (pttt) REVERT: C 92 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8023 (tt0) REVERT: C 112 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 203 GLN cc_start: 0.8104 (tp40) cc_final: 0.7895 (tm-30) REVERT: C 220 GLU cc_start: 0.8253 (pp20) cc_final: 0.7870 (pp20) REVERT: C 278 LYS cc_start: 0.8445 (ptpt) cc_final: 0.7885 (pttt) REVERT: D 92 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8084 (tt0) REVERT: D 112 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8804 (tm-30) REVERT: D 202 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8375 (mtpt) REVERT: D 203 GLN cc_start: 0.8069 (tp40) cc_final: 0.7791 (tm-30) REVERT: D 278 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7627 (ptpt) REVERT: E 75 TYR cc_start: 0.8176 (m-10) cc_final: 0.7901 (m-80) REVERT: E 92 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8109 (tt0) REVERT: E 278 LYS cc_start: 0.8319 (ptmt) cc_final: 0.7608 (ptpt) REVERT: F 112 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8787 (tm-30) REVERT: F 134 GLU cc_start: 0.8173 (tt0) cc_final: 0.7888 (tt0) REVERT: F 202 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8657 (mtpp) REVERT: F 203 GLN cc_start: 0.8012 (tp40) cc_final: 0.7576 (tm-30) REVERT: F 212 GLU cc_start: 0.7909 (tp30) cc_final: 0.7630 (tp30) REVERT: G 75 TYR cc_start: 0.8059 (m-10) cc_final: 0.7830 (m-10) REVERT: G 92 GLN cc_start: 0.8761 (mm-40) cc_final: 0.7965 (tt0) REVERT: G 112 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8841 (tm-30) REVERT: G 255 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7689 (tm-30) REVERT: G 278 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7979 (ptpt) outliers start: 10 outliers final: 6 residues processed: 222 average time/residue: 0.3008 time to fit residues: 94.8390 Evaluate side-chains 193 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain G residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN B 207 ASN C 21 GLN D 21 GLN E 21 GLN F 21 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15554 Z= 0.328 Angle : 0.541 6.156 20993 Z= 0.288 Chirality : 0.042 0.143 2520 Planarity : 0.003 0.024 2625 Dihedral : 11.326 68.689 2513 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 11.77 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.19), residues: 1946 helix: 1.54 (0.16), residues: 1001 sheet: -0.17 (0.34), residues: 273 loop : -2.01 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 16 PHE 0.008 0.001 PHE B 130 TYR 0.011 0.001 TYR D 250 ARG 0.003 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 204 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8345 (mtpt) REVERT: A 203 GLN cc_start: 0.8178 (tp40) cc_final: 0.7954 (tm-30) REVERT: B 20 ASN cc_start: 0.8816 (t0) cc_final: 0.8593 (t0) REVERT: B 134 GLU cc_start: 0.8277 (tt0) cc_final: 0.7866 (tt0) REVERT: B 203 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 278 LYS cc_start: 0.8346 (ptmt) cc_final: 0.7625 (pttt) REVERT: C 112 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8778 (tm-30) REVERT: C 203 GLN cc_start: 0.8202 (tp40) cc_final: 0.7769 (tm-30) REVERT: D 92 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8149 (tt0) REVERT: D 112 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8832 (tm-30) REVERT: D 203 GLN cc_start: 0.8251 (tp40) cc_final: 0.7878 (tm-30) REVERT: D 278 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7544 (ptpt) REVERT: E 75 TYR cc_start: 0.8194 (m-10) cc_final: 0.7920 (m-80) REVERT: E 92 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8166 (tt0) REVERT: E 278 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7673 (ptpt) REVERT: F 112 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8773 (tm-30) REVERT: F 134 GLU cc_start: 0.8198 (tt0) cc_final: 0.7957 (tt0) REVERT: F 202 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8592 (mtpp) REVERT: F 203 GLN cc_start: 0.8070 (tp40) cc_final: 0.7618 (tm-30) REVERT: F 212 GLU cc_start: 0.7922 (tp30) cc_final: 0.7637 (tp30) REVERT: G 75 TYR cc_start: 0.8093 (m-10) cc_final: 0.7877 (m-10) REVERT: G 92 GLN cc_start: 0.8735 (mm-40) cc_final: 0.7917 (tt0) REVERT: G 112 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8833 (tm-30) REVERT: G 255 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: G 278 LYS cc_start: 0.8028 (ptmt) cc_final: 0.7788 (ptpt) outliers start: 51 outliers final: 24 residues processed: 233 average time/residue: 0.2989 time to fit residues: 99.2572 Evaluate side-chains 208 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN C 21 GLN D 21 GLN E 21 GLN G 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15554 Z= 0.203 Angle : 0.484 7.773 20993 Z= 0.255 Chirality : 0.041 0.134 2520 Planarity : 0.002 0.022 2625 Dihedral : 10.919 67.036 2513 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 11.83 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.19), residues: 1946 helix: 1.88 (0.16), residues: 1001 sheet: 0.02 (0.33), residues: 273 loop : -1.75 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 16 PHE 0.007 0.001 PHE G 277 TYR 0.007 0.001 TYR D 250 ARG 0.004 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5922 (tpt) cc_final: 0.5557 (tpt) REVERT: A 112 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8641 (pp30) REVERT: A 202 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8344 (mtpt) REVERT: B 92 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8112 (tt0) REVERT: B 134 GLU cc_start: 0.8261 (tt0) cc_final: 0.7745 (tt0) REVERT: B 278 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7632 (pttt) REVERT: C 92 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8029 (tt0) REVERT: C 112 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8759 (tm-30) REVERT: C 203 GLN cc_start: 0.8152 (tp40) cc_final: 0.7747 (tm-30) REVERT: D 1 MET cc_start: 0.6078 (tpt) cc_final: 0.5825 (tpt) REVERT: D 92 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8147 (tt0) REVERT: D 112 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 203 GLN cc_start: 0.8133 (tp40) cc_final: 0.7817 (tm-30) REVERT: D 278 LYS cc_start: 0.8087 (ptmt) cc_final: 0.7492 (ptpt) REVERT: E 75 TYR cc_start: 0.8151 (m-10) cc_final: 0.7870 (m-80) REVERT: E 92 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8164 (tt0) REVERT: E 278 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7653 (ptpt) REVERT: F 20 ASN cc_start: 0.8698 (t0) cc_final: 0.8372 (t0) REVERT: F 112 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8767 (tm-30) REVERT: F 203 GLN cc_start: 0.8044 (tp40) cc_final: 0.7613 (tm-30) REVERT: F 212 GLU cc_start: 0.7916 (tp30) cc_final: 0.7641 (tp30) REVERT: G 20 ASN cc_start: 0.8704 (t0) cc_final: 0.8481 (t0) REVERT: G 75 TYR cc_start: 0.8044 (m-10) cc_final: 0.7818 (m-10) REVERT: G 92 GLN cc_start: 0.8701 (mm-40) cc_final: 0.7982 (tt0) REVERT: G 112 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8803 (tm-30) REVERT: G 255 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: G 278 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7773 (ptpt) outliers start: 41 outliers final: 24 residues processed: 235 average time/residue: 0.3020 time to fit residues: 100.5699 Evaluate side-chains 218 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN C 21 GLN D 21 GLN E 21 GLN G 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15554 Z= 0.136 Angle : 0.462 7.951 20993 Z= 0.242 Chirality : 0.040 0.140 2520 Planarity : 0.002 0.020 2625 Dihedral : 10.496 63.467 2513 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.01 % Allowed : 14.35 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.19), residues: 1946 helix: 2.10 (0.16), residues: 1008 sheet: 0.15 (0.32), residues: 273 loop : -1.53 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 16 PHE 0.006 0.001 PHE G 235 TYR 0.004 0.001 TYR F 27 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5703 (tpt) cc_final: 0.5347 (tpt) REVERT: A 112 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8580 (pp30) REVERT: A 202 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8480 (mtpp) REVERT: A 203 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 20 ASN cc_start: 0.8837 (t0) cc_final: 0.8616 (m-40) REVERT: B 92 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8096 (tt0) REVERT: B 112 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8596 (pp30) REVERT: B 134 GLU cc_start: 0.8269 (tt0) cc_final: 0.7891 (tt0) REVERT: B 278 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7661 (pttt) REVERT: C 92 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8036 (tt0) REVERT: C 112 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8658 (tm-30) REVERT: C 203 GLN cc_start: 0.8211 (tp40) cc_final: 0.7774 (tm-30) REVERT: D 1 MET cc_start: 0.5826 (tpt) cc_final: 0.5325 (tpt) REVERT: D 21 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: D 92 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8221 (tt0) REVERT: D 112 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8757 (tm-30) REVERT: D 203 GLN cc_start: 0.8052 (tp40) cc_final: 0.7705 (tm-30) REVERT: E 21 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: E 75 TYR cc_start: 0.8103 (m-10) cc_final: 0.7817 (m-80) REVERT: E 92 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8287 (tt0) REVERT: F 20 ASN cc_start: 0.8768 (t0) cc_final: 0.8419 (t0) REVERT: F 92 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8229 (tt0) REVERT: F 203 GLN cc_start: 0.8042 (tp40) cc_final: 0.7684 (tm-30) REVERT: F 212 GLU cc_start: 0.7877 (tp30) cc_final: 0.7609 (tp30) REVERT: G 1 MET cc_start: 0.6212 (tmm) cc_final: 0.4877 (tmm) REVERT: G 20 ASN cc_start: 0.8652 (t0) cc_final: 0.8411 (t0) REVERT: G 21 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: G 75 TYR cc_start: 0.7975 (m-10) cc_final: 0.7743 (m-10) REVERT: G 92 GLN cc_start: 0.8669 (mm-40) cc_final: 0.7965 (tt0) REVERT: G 112 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8728 (tm-30) REVERT: G 255 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: G 278 LYS cc_start: 0.7986 (ptmt) cc_final: 0.7764 (ptpt) outliers start: 32 outliers final: 15 residues processed: 227 average time/residue: 0.3075 time to fit residues: 98.6571 Evaluate side-chains 215 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 0.0030 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN C 21 GLN D 21 GLN E 21 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN G 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15554 Z= 0.161 Angle : 0.466 6.869 20993 Z= 0.246 Chirality : 0.041 0.148 2520 Planarity : 0.002 0.021 2625 Dihedral : 10.330 60.386 2513 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.95 % Allowed : 14.85 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.19), residues: 1946 helix: 2.20 (0.16), residues: 1008 sheet: 0.29 (0.32), residues: 273 loop : -1.42 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 16 PHE 0.011 0.001 PHE G 127 TYR 0.007 0.001 TYR C 250 ARG 0.004 0.000 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8054 (tt0) REVERT: A 112 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8557 (pp30) REVERT: A 202 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8427 (mtpt) REVERT: A 203 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 20 ASN cc_start: 0.8839 (t0) cc_final: 0.8570 (p0) REVERT: B 92 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8079 (tt0) REVERT: B 134 GLU cc_start: 0.8282 (tt0) cc_final: 0.7891 (tt0) REVERT: B 278 LYS cc_start: 0.8272 (ptmt) cc_final: 0.7641 (pttt) REVERT: C 56 MET cc_start: 0.7787 (ppp) cc_final: 0.7563 (ppp) REVERT: C 92 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8046 (tt0) REVERT: C 112 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8639 (tm-30) REVERT: D 1 MET cc_start: 0.5787 (tpt) cc_final: 0.5409 (tpt) REVERT: D 92 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8221 (tt0) REVERT: D 112 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8751 (tm-30) REVERT: D 203 GLN cc_start: 0.8043 (tp40) cc_final: 0.7655 (tm-30) REVERT: D 278 LYS cc_start: 0.8011 (ptmt) cc_final: 0.7420 (ptpt) REVERT: E 56 MET cc_start: 0.7952 (ppp) cc_final: 0.7749 (ppp) REVERT: E 75 TYR cc_start: 0.8074 (m-10) cc_final: 0.7789 (m-80) REVERT: E 92 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8270 (tt0) REVERT: E 169 LYS cc_start: 0.9124 (tttm) cc_final: 0.8843 (tttm) REVERT: F 20 ASN cc_start: 0.8762 (t0) cc_final: 0.8421 (t0) REVERT: F 92 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8154 (tt0) REVERT: F 203 GLN cc_start: 0.8054 (tp40) cc_final: 0.7692 (tm-30) REVERT: F 212 GLU cc_start: 0.7962 (tp30) cc_final: 0.7642 (tp30) REVERT: G 20 ASN cc_start: 0.8735 (t0) cc_final: 0.8487 (t0) REVERT: G 21 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8635 (mt0) REVERT: G 75 TYR cc_start: 0.7961 (m-10) cc_final: 0.7731 (m-10) REVERT: G 92 GLN cc_start: 0.8648 (mm-40) cc_final: 0.7944 (tt0) REVERT: G 112 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8725 (tm-30) REVERT: G 255 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: G 278 LYS cc_start: 0.7984 (ptmt) cc_final: 0.7759 (ptpt) outliers start: 31 outliers final: 19 residues processed: 221 average time/residue: 0.2947 time to fit residues: 92.8669 Evaluate side-chains 214 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 9.9990 chunk 21 optimal weight: 0.0050 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN C 21 GLN D 21 GLN E 21 GLN F 21 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15554 Z= 0.138 Angle : 0.459 6.807 20993 Z= 0.242 Chirality : 0.041 0.149 2520 Planarity : 0.002 0.021 2625 Dihedral : 10.122 59.990 2513 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 15.48 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.19), residues: 1946 helix: 2.30 (0.16), residues: 1008 sheet: 0.39 (0.32), residues: 273 loop : -1.31 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 16 PHE 0.008 0.001 PHE G 127 TYR 0.006 0.001 TYR F 27 ARG 0.004 0.000 ARG E 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8035 (tt0) REVERT: A 112 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8516 (pp30) REVERT: A 202 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8443 (mtpt) REVERT: A 203 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 20 ASN cc_start: 0.8818 (t0) cc_final: 0.8537 (p0) REVERT: B 92 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8115 (tt0) REVERT: B 112 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8542 (pp30) REVERT: B 134 GLU cc_start: 0.8285 (tt0) cc_final: 0.7906 (tt0) REVERT: B 278 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7679 (pttt) REVERT: C 92 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8043 (tt0) REVERT: C 112 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8609 (tm-30) REVERT: C 169 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9096 (ttpp) REVERT: D 1 MET cc_start: 0.5704 (tpt) cc_final: 0.5339 (tpt) REVERT: D 21 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: D 92 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8216 (tt0) REVERT: D 112 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8681 (tm-30) REVERT: D 203 GLN cc_start: 0.8026 (tp40) cc_final: 0.7700 (tm-30) REVERT: D 278 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7431 (ptpt) REVERT: E 21 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: E 68 PHE cc_start: 0.7870 (m-80) cc_final: 0.7563 (m-10) REVERT: E 75 TYR cc_start: 0.7996 (m-10) cc_final: 0.7713 (m-80) REVERT: E 92 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8255 (tt0) REVERT: E 112 GLN cc_start: 0.8913 (pp30) cc_final: 0.8537 (pp30) REVERT: E 169 LYS cc_start: 0.9130 (tttm) cc_final: 0.8861 (tttm) REVERT: F 20 ASN cc_start: 0.8757 (t0) cc_final: 0.8523 (p0) REVERT: F 92 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8125 (tt0) REVERT: F 112 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8609 (pp30) REVERT: F 203 GLN cc_start: 0.8035 (tp40) cc_final: 0.7679 (tm-30) REVERT: F 212 GLU cc_start: 0.7938 (tp30) cc_final: 0.7625 (tp30) REVERT: G 20 ASN cc_start: 0.8750 (t0) cc_final: 0.8489 (t0) REVERT: G 21 GLN cc_start: 0.8783 (pt0) cc_final: 0.8252 (mt0) REVERT: G 75 TYR cc_start: 0.7928 (m-10) cc_final: 0.7699 (m-10) REVERT: G 92 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7937 (tt0) REVERT: G 112 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8693 (tm-30) REVERT: G 255 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: G 278 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7717 (ptpt) outliers start: 31 outliers final: 20 residues processed: 224 average time/residue: 0.2886 time to fit residues: 93.1844 Evaluate side-chains 218 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 0.0870 chunk 112 optimal weight: 40.0000 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 207 ASN B 21 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN F 21 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15554 Z= 0.154 Angle : 0.470 6.913 20993 Z= 0.247 Chirality : 0.041 0.147 2520 Planarity : 0.002 0.020 2625 Dihedral : 9.986 59.826 2513 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.89 % Allowed : 15.80 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.20), residues: 1946 helix: 2.34 (0.16), residues: 1008 sheet: 0.45 (0.32), residues: 273 loop : -1.25 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 16 PHE 0.007 0.001 PHE G 127 TYR 0.008 0.001 TYR D 250 ARG 0.004 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5626 (tpt) cc_final: 0.5244 (tpt) REVERT: A 21 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: A 92 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8025 (tt0) REVERT: A 112 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8523 (pp30) REVERT: A 202 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8437 (mtpt) REVERT: A 203 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 20 ASN cc_start: 0.8812 (t0) cc_final: 0.8406 (t0) REVERT: B 92 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8115 (tt0) REVERT: B 112 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8547 (pp30) REVERT: B 134 GLU cc_start: 0.8228 (tt0) cc_final: 0.7806 (tt0) REVERT: B 278 LYS cc_start: 0.8276 (ptmt) cc_final: 0.7818 (pttt) REVERT: C 92 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8038 (tt0) REVERT: C 112 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 278 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7885 (ptpt) REVERT: D 92 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8217 (tt0) REVERT: D 112 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8687 (tm-30) REVERT: D 203 GLN cc_start: 0.8061 (tp40) cc_final: 0.7676 (tm-30) REVERT: D 278 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7418 (ptpt) REVERT: E 68 PHE cc_start: 0.7867 (m-80) cc_final: 0.7560 (m-10) REVERT: E 75 TYR cc_start: 0.7987 (m-10) cc_final: 0.7704 (m-80) REVERT: E 92 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8210 (tt0) REVERT: E 112 GLN cc_start: 0.8900 (pp30) cc_final: 0.8640 (pp30) REVERT: E 169 LYS cc_start: 0.9143 (tttm) cc_final: 0.8871 (tttm) REVERT: E 203 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7682 (tm-30) REVERT: F 20 ASN cc_start: 0.8754 (t0) cc_final: 0.8395 (t0) REVERT: F 92 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8122 (tt0) REVERT: F 112 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8605 (pp30) REVERT: F 203 GLN cc_start: 0.8050 (tp40) cc_final: 0.7688 (tm-30) REVERT: F 212 GLU cc_start: 0.7936 (tp30) cc_final: 0.7630 (tp30) REVERT: G 20 ASN cc_start: 0.8732 (t0) cc_final: 0.8440 (t0) REVERT: G 21 GLN cc_start: 0.8776 (pt0) cc_final: 0.8251 (mt0) REVERT: G 75 TYR cc_start: 0.7914 (m-10) cc_final: 0.7690 (m-10) REVERT: G 92 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7926 (tt0) REVERT: G 112 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8699 (tm-30) REVERT: G 155 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7915 (ptm) REVERT: G 255 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: G 278 LYS cc_start: 0.7953 (ptmt) cc_final: 0.7719 (ptpt) outliers start: 30 outliers final: 24 residues processed: 218 average time/residue: 0.2899 time to fit residues: 90.6746 Evaluate side-chains 220 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 8.9990 chunk 180 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN C 21 GLN D 21 GLN E 21 GLN F 21 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15554 Z= 0.151 Angle : 0.465 7.757 20993 Z= 0.244 Chirality : 0.041 0.149 2520 Planarity : 0.002 0.020 2625 Dihedral : 9.864 59.565 2513 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 16.11 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.20), residues: 1946 helix: 2.38 (0.16), residues: 1008 sheet: 0.48 (0.32), residues: 273 loop : -1.21 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 16 PHE 0.010 0.001 PHE B 127 TYR 0.007 0.001 TYR D 250 ARG 0.004 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: A 92 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8018 (tt0) REVERT: A 112 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8524 (pp30) REVERT: A 202 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8437 (mtpt) REVERT: A 203 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 20 ASN cc_start: 0.8842 (t0) cc_final: 0.8533 (t0) REVERT: B 92 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8100 (tt0) REVERT: B 112 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8544 (pp30) REVERT: B 134 GLU cc_start: 0.8206 (tt0) cc_final: 0.7795 (tt0) REVERT: C 21 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: C 92 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8040 (tt0) REVERT: C 112 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8609 (tm-30) REVERT: C 278 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7889 (ptpt) REVERT: D 21 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: D 92 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8218 (tt0) REVERT: D 112 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8688 (tm-30) REVERT: D 203 GLN cc_start: 0.8064 (tp40) cc_final: 0.7676 (tm-30) REVERT: D 278 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7408 (ptpt) REVERT: E 21 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8076 (mp10) REVERT: E 68 PHE cc_start: 0.7871 (m-80) cc_final: 0.7567 (m-10) REVERT: E 75 TYR cc_start: 0.8003 (m-10) cc_final: 0.7725 (m-10) REVERT: E 92 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8219 (tt0) REVERT: E 112 GLN cc_start: 0.8933 (pp30) cc_final: 0.8632 (pp30) REVERT: E 169 LYS cc_start: 0.9144 (tttm) cc_final: 0.8882 (tttm) REVERT: F 20 ASN cc_start: 0.8791 (t0) cc_final: 0.8436 (t0) REVERT: F 21 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: F 75 TYR cc_start: 0.8033 (m-10) cc_final: 0.7814 (m-10) REVERT: F 92 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8096 (tt0) REVERT: F 112 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8644 (pp30) REVERT: F 203 GLN cc_start: 0.8047 (tp40) cc_final: 0.7685 (tm-30) REVERT: F 212 GLU cc_start: 0.7942 (tp30) cc_final: 0.7641 (tp30) REVERT: G 20 ASN cc_start: 0.8714 (t0) cc_final: 0.8410 (t0) REVERT: G 21 GLN cc_start: 0.8776 (pt0) cc_final: 0.8266 (mt0) REVERT: G 75 TYR cc_start: 0.7937 (m-10) cc_final: 0.7711 (m-10) REVERT: G 92 GLN cc_start: 0.8616 (mm-40) cc_final: 0.7925 (tt0) REVERT: G 112 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8699 (tm-30) REVERT: G 155 MET cc_start: 0.8286 (ptp) cc_final: 0.7869 (ptm) REVERT: G 278 LYS cc_start: 0.7939 (ptmt) cc_final: 0.7698 (ptpt) outliers start: 30 outliers final: 19 residues processed: 218 average time/residue: 0.2835 time to fit residues: 89.4688 Evaluate side-chains 217 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 0.0000 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 21 GLN E 21 GLN E 203 GLN E 207 ASN F 21 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15554 Z= 0.153 Angle : 0.476 8.719 20993 Z= 0.248 Chirality : 0.041 0.154 2520 Planarity : 0.002 0.020 2625 Dihedral : 9.770 59.750 2513 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 16.17 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.20), residues: 1946 helix: 2.42 (0.16), residues: 1008 sheet: 0.51 (0.32), residues: 273 loop : -1.21 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 16 PHE 0.011 0.001 PHE B 277 TYR 0.007 0.001 TYR D 250 ARG 0.005 0.000 ARG E 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: A 92 GLN cc_start: 0.8687 (mm-40) cc_final: 0.7979 (tt0) REVERT: A 112 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8524 (pp30) REVERT: A 202 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8435 (mtpt) REVERT: A 203 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 20 ASN cc_start: 0.8778 (t0) cc_final: 0.8415 (p0) REVERT: B 21 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: B 92 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8109 (tt0) REVERT: B 112 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8520 (pp30) REVERT: B 134 GLU cc_start: 0.8212 (tt0) cc_final: 0.7774 (tt0) REVERT: B 278 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7450 (pttt) REVERT: C 21 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: C 92 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8046 (tt0) REVERT: C 112 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 278 LYS cc_start: 0.8408 (ptpt) cc_final: 0.7896 (ptpt) REVERT: D 21 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: D 92 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8218 (tt0) REVERT: D 112 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8687 (tm-30) REVERT: D 203 GLN cc_start: 0.8063 (tp40) cc_final: 0.7654 (tm-30) REVERT: D 278 LYS cc_start: 0.7902 (ptmt) cc_final: 0.7356 (ptpt) REVERT: E 21 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: E 68 PHE cc_start: 0.7876 (m-80) cc_final: 0.7574 (m-10) REVERT: E 75 TYR cc_start: 0.7947 (m-10) cc_final: 0.7680 (m-10) REVERT: E 92 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8220 (tt0) REVERT: E 112 GLN cc_start: 0.8923 (pp30) cc_final: 0.8618 (pp30) REVERT: E 169 LYS cc_start: 0.9142 (tttm) cc_final: 0.8880 (tttm) REVERT: F 20 ASN cc_start: 0.8820 (t0) cc_final: 0.8556 (t0) REVERT: F 75 TYR cc_start: 0.8032 (m-10) cc_final: 0.7817 (m-10) REVERT: F 92 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8061 (tt0) REVERT: F 112 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8643 (pp30) REVERT: F 203 GLN cc_start: 0.8044 (tp40) cc_final: 0.7696 (tm-30) REVERT: F 212 GLU cc_start: 0.7944 (tp30) cc_final: 0.7641 (tp30) REVERT: G 20 ASN cc_start: 0.8689 (t0) cc_final: 0.8387 (t0) REVERT: G 21 GLN cc_start: 0.8786 (pt0) cc_final: 0.8254 (mt0) REVERT: G 75 TYR cc_start: 0.7937 (m-10) cc_final: 0.7718 (m-10) REVERT: G 92 GLN cc_start: 0.8605 (mm-40) cc_final: 0.7907 (tt0) REVERT: G 112 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8699 (tm-30) REVERT: G 155 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7852 (ptm) REVERT: G 278 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7693 (ptpt) outliers start: 31 outliers final: 20 residues processed: 213 average time/residue: 0.2796 time to fit residues: 86.8455 Evaluate side-chains 219 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN C 21 GLN D 21 GLN E 21 GLN F 21 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064592 restraints weight = 32946.581| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.67 r_work: 0.2862 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15554 Z= 0.349 Angle : 0.554 8.757 20993 Z= 0.290 Chirality : 0.043 0.150 2520 Planarity : 0.003 0.027 2625 Dihedral : 10.075 62.999 2513 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.20 % Allowed : 16.17 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.19), residues: 1946 helix: 2.16 (0.16), residues: 1008 sheet: 0.37 (0.33), residues: 273 loop : -1.36 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 16 PHE 0.008 0.001 PHE B 277 TYR 0.015 0.001 TYR D 250 ARG 0.005 0.000 ARG E 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.44 seconds wall clock time: 58 minutes 52.42 seconds (3532.42 seconds total)