Starting phenix.real_space_refine on Sat Mar 16 15:44:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/03_2024/6vx6_21431.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/03_2024/6vx6_21431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/03_2024/6vx6_21431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/03_2024/6vx6_21431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/03_2024/6vx6_21431.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/03_2024/6vx6_21431.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 95 5.16 5 Cl 1 4.86 5 C 9870 2.51 5 N 2485 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E ASP 270": "OD1" <-> "OD2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E ARG 344": "NH1" <-> "NH2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D PHE 353": "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: 15061 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "A" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "B" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "C" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "D" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.48, per 1000 atoms: 0.50 Number of scatterers: 15061 At special positions: 0 Unit cell: (97.94, 96.28, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 95 16.00 O 2605 8.00 N 2485 7.00 C 9870 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: 4.82 Conformation dependent library (CDL) restraints added in 2.5 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 69.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA E 10 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU E 22 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.533A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.790A pdb=" N CYS E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU A 22 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 37 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.789A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 4.346A pdb=" N SER A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA B 10 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.726A pdb=" N LEU B 22 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 37 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.654A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA C 10 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU C 22 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 37 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.725A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA D 10 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU D 22 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 37 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4103 1.33 - 1.45: 3153 1.45 - 1.57: 8069 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 15470 Sorted by residual: bond pdb=" N VAL A 183 " pdb=" CA VAL A 183 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.90e+00 bond pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.75e+00 bond pdb=" N VAL E 183 " pdb=" CA VAL E 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.58e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.51e+00 bond pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.47e+00 ... (remaining 15465 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.89: 380 106.89 - 113.75: 8080 113.75 - 120.60: 7086 120.60 - 127.45: 5275 127.45 - 134.30: 159 Bond angle restraints: 20980 Sorted by residual: angle pdb=" N LEU B 88 " pdb=" CA LEU B 88 " pdb=" C LEU B 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU D 88 " pdb=" CA LEU D 88 " pdb=" C LEU D 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU E 88 " pdb=" CA LEU E 88 " pdb=" C LEU E 88 " ideal model delta sigma weight residual 111.82 106.42 5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N LEU A 88 " pdb=" CA LEU A 88 " pdb=" C LEU A 88 " ideal model delta sigma weight residual 111.82 106.43 5.39 1.16e+00 7.43e-01 2.16e+01 angle pdb=" N LEU C 88 " pdb=" CA LEU C 88 " pdb=" C LEU C 88 " ideal model delta sigma weight residual 111.82 106.44 5.38 1.16e+00 7.43e-01 2.15e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 7840 15.45 - 30.91: 910 30.91 - 46.36: 155 46.36 - 61.82: 45 61.82 - 77.27: 25 Dihedral angle restraints: 8975 sinusoidal: 3575 harmonic: 5400 Sorted by residual: dihedral pdb=" C VAL A 183 " pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" CB VAL A 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL D 183 " pdb=" N VAL D 183 " pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL C 183 " pdb=" N VAL C 183 " pdb=" CA VAL C 183 " pdb=" CB VAL C 183 " ideal model delta harmonic sigma weight residual -122.00 -131.83 9.83 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1739 0.053 - 0.105: 419 0.105 - 0.158: 76 0.158 - 0.210: 26 0.210 - 0.263: 15 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO C 77 " pdb=" N PRO C 77 " pdb=" C PRO C 77 " pdb=" CB PRO C 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO D 77 " pdb=" N PRO D 77 " pdb=" C PRO D 77 " pdb=" CB PRO D 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO E 77 " pdb=" N PRO E 77 " pdb=" C PRO E 77 " pdb=" CB PRO E 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2272 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 351 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C THR A 351 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 351 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 352 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C THR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 352 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 351 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C THR C 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 351 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 352 " -0.016 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4107 2.79 - 3.32: 12796 3.32 - 3.84: 25125 3.84 - 4.37: 32863 4.37 - 4.90: 53533 Nonbonded interactions: 128424 Sorted by model distance: nonbonded pdb=" O ASN C 296 " pdb="CA CA C 501 " model vdw 2.260 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 501 " model vdw 2.273 2.510 nonbonded pdb=" O ALA C 10 " pdb="CA CA D 501 " model vdw 2.277 2.510 nonbonded pdb=" O LEU A 75 " pdb=" OH TYR A 284 " model vdw 2.289 2.440 nonbonded pdb=" O LEU B 75 " pdb=" OH TYR B 284 " model vdw 2.289 2.440 ... (remaining 128419 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 2 through 367) selection = (chain 'B' and resid 2 through 367) selection = (chain 'C' and resid 2 through 367) selection = (chain 'D' and resid 2 through 367) selection = (chain 'E' and resid 2 through 367) } 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.370 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 36.520 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15470 Z= 0.300 Angle : 0.819 9.563 20980 Z= 0.492 Chirality : 0.053 0.263 2275 Planarity : 0.004 0.040 2625 Dihedral : 14.085 77.272 5505 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % 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: -5.69 (0.12), residues: 1820 helix: -4.58 (0.05), residues: 1055 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 93 HIS 0.002 0.000 HIS D 115 PHE 0.020 0.002 PHE D 282 TYR 0.031 0.002 TYR D 236 ARG 0.019 0.001 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 263 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7512 (mpt180) REVERT: A 175 ASN cc_start: 0.7994 (t0) cc_final: 0.7779 (m-40) REVERT: A 203 ASP cc_start: 0.7708 (m-30) cc_final: 0.7471 (m-30) REVERT: D 64 LYS cc_start: 0.7760 (mttm) cc_final: 0.7468 (mtpt) REVERT: D 68 TYR cc_start: 0.7975 (t80) cc_final: 0.7760 (t80) outliers start: 15 outliers final: 0 residues processed: 278 average time/residue: 1.4611 time to fit residues: 440.9549 Evaluate side-chains 162 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 293 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 296 ASN A 361 GLN B 58 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 293 GLN D 361 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15470 Z= 0.280 Angle : 0.591 11.203 20980 Z= 0.303 Chirality : 0.040 0.136 2275 Planarity : 0.004 0.026 2625 Dihedral : 4.355 15.017 2055 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.08 % Allowed : 14.53 % Favored : 83.40 % 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: -3.07 (0.15), residues: 1820 helix: -2.13 (0.12), residues: 1090 sheet: None (None), residues: 0 loop : -1.62 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 182 HIS 0.002 0.000 HIS B 115 PHE 0.019 0.002 PHE E 283 TYR 0.024 0.002 TYR D 236 ARG 0.005 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7156 (m-10) cc_final: 0.6906 (m-10) REVERT: A 203 ASP cc_start: 0.7773 (m-30) cc_final: 0.7468 (m-30) REVERT: A 334 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.7900 (mmtp) REVERT: B 64 LYS cc_start: 0.7629 (mttm) cc_final: 0.7255 (mtpt) REVERT: B 163 MET cc_start: 0.9340 (ttm) cc_final: 0.9112 (ttp) outliers start: 33 outliers final: 9 residues processed: 201 average time/residue: 1.2894 time to fit residues: 286.0374 Evaluate side-chains 171 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.200 Angle : 0.504 10.741 20980 Z= 0.255 Chirality : 0.038 0.119 2275 Planarity : 0.003 0.022 2625 Dihedral : 3.989 15.365 2055 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.64 % Allowed : 15.09 % Favored : 82.26 % 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 (0.17), residues: 1820 helix: -0.60 (0.14), residues: 1095 sheet: None (None), residues: 0 loop : -1.36 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 PHE 0.022 0.001 PHE E 80 TYR 0.013 0.001 TYR D 236 ARG 0.005 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: A 203 ASP cc_start: 0.7796 (m-30) cc_final: 0.7441 (m-30) REVERT: A 334 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7956 (mmtp) REVERT: B 34 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7480 (mtt90) REVERT: B 64 LYS cc_start: 0.7629 (mttm) cc_final: 0.7303 (mtpt) REVERT: B 163 MET cc_start: 0.9274 (ttm) cc_final: 0.9071 (ttp) REVERT: C 64 LYS cc_start: 0.7830 (mttm) cc_final: 0.7517 (mtpt) REVERT: C 165 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7244 (mpt180) REVERT: D 11 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8125 (ttpt) REVERT: D 68 TYR cc_start: 0.7996 (t80) cc_final: 0.7670 (t80) outliers start: 42 outliers final: 15 residues processed: 216 average time/residue: 1.3238 time to fit residues: 313.9568 Evaluate side-chains 192 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 296 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.187 Angle : 0.503 11.656 20980 Z= 0.248 Chirality : 0.038 0.117 2275 Planarity : 0.003 0.022 2625 Dihedral : 3.855 15.158 2055 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.70 % Allowed : 15.72 % Favored : 81.57 % 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: -0.60 (0.18), residues: 1820 helix: 0.14 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.004 0.001 HIS A 91 PHE 0.019 0.001 PHE B 276 TYR 0.012 0.001 TYR C 236 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 ASN cc_start: 0.8802 (m-40) cc_final: 0.8578 (m-40) REVERT: E 168 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7706 (ttm170) REVERT: E 262 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7597 (mm110) REVERT: A 175 ASN cc_start: 0.7965 (t0) cc_final: 0.7574 (m-40) REVERT: A 203 ASP cc_start: 0.7798 (m-30) cc_final: 0.7432 (m-30) REVERT: A 334 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7972 (mmtp) REVERT: B 64 LYS cc_start: 0.7634 (mttm) cc_final: 0.7350 (mtpt) REVERT: B 163 MET cc_start: 0.9245 (ttm) cc_final: 0.9028 (ttp) REVERT: C 64 LYS cc_start: 0.7740 (mttm) cc_final: 0.7442 (mtpt) REVERT: C 165 ARG cc_start: 0.7668 (tpp-160) cc_final: 0.7302 (mpt180) REVERT: D 68 TYR cc_start: 0.8028 (t80) cc_final: 0.7820 (t80) outliers start: 43 outliers final: 21 residues processed: 220 average time/residue: 1.2652 time to fit residues: 307.2126 Evaluate side-chains 200 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN D 95 ASN D 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15470 Z= 0.400 Angle : 0.604 11.110 20980 Z= 0.300 Chirality : 0.044 0.145 2275 Planarity : 0.003 0.053 2625 Dihedral : 4.100 16.657 2055 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.08 % Allowed : 16.29 % Favored : 80.63 % 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: -0.37 (0.18), residues: 1820 helix: 0.28 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -0.99 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 182 HIS 0.003 0.001 HIS D 91 PHE 0.023 0.002 PHE D 283 TYR 0.024 0.002 TYR A 236 ARG 0.013 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: E 262 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7573 (mm110) REVERT: A 168 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7415 (ttm170) REVERT: A 203 ASP cc_start: 0.7890 (m-30) cc_final: 0.7588 (m-30) REVERT: A 334 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8650 (mttp) REVERT: B 64 LYS cc_start: 0.7608 (mttm) cc_final: 0.7378 (mtpt) REVERT: B 177 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 64 LYS cc_start: 0.7812 (mttm) cc_final: 0.7536 (mtpt) REVERT: C 165 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7376 (mpt180) REVERT: D 63 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: D 68 TYR cc_start: 0.8117 (t80) cc_final: 0.7914 (t80) outliers start: 49 outliers final: 29 residues processed: 205 average time/residue: 1.2950 time to fit residues: 292.2357 Evaluate side-chains 202 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN B 308 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15470 Z= 0.151 Angle : 0.496 11.976 20980 Z= 0.245 Chirality : 0.037 0.141 2275 Planarity : 0.002 0.021 2625 Dihedral : 3.810 14.794 2055 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.33 % Allowed : 17.48 % Favored : 80.19 % 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: 0.13 (0.19), residues: 1820 helix: 0.75 (0.15), residues: 1155 sheet: None (None), residues: 0 loop : -1.00 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 PHE 0.018 0.001 PHE C 276 TYR 0.009 0.001 TYR C 337 ARG 0.004 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 ASN cc_start: 0.8803 (m-40) cc_final: 0.8585 (m-40) REVERT: E 168 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: E 262 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7600 (mm110) REVERT: A 168 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7283 (ttm110) REVERT: A 175 ASN cc_start: 0.7974 (t0) cc_final: 0.7602 (m-40) REVERT: A 203 ASP cc_start: 0.7831 (m-30) cc_final: 0.7551 (m-30) REVERT: A 334 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8627 (mttp) REVERT: B 64 LYS cc_start: 0.7704 (mttm) cc_final: 0.7487 (mtpt) REVERT: B 177 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8541 (p) REVERT: C 64 LYS cc_start: 0.7687 (mttm) cc_final: 0.7425 (mtpt) REVERT: C 165 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7318 (mpt180) REVERT: D 63 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7890 (mt-10) outliers start: 37 outliers final: 20 residues processed: 217 average time/residue: 1.2563 time to fit residues: 300.5412 Evaluate side-chains 202 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN B 308 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.198 Angle : 0.508 11.329 20980 Z= 0.252 Chirality : 0.038 0.135 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.790 14.551 2055 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.20 % Allowed : 18.11 % Favored : 79.69 % 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: 0.27 (0.19), residues: 1820 helix: 0.82 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.95 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 PHE 0.025 0.001 PHE E 80 TYR 0.017 0.001 TYR D 68 ARG 0.003 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 71 ARG cc_start: 0.7922 (ptm160) cc_final: 0.7624 (ptm-80) REVERT: E 95 ASN cc_start: 0.8815 (m-40) cc_final: 0.8599 (m-40) REVERT: E 168 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7743 (ttm170) REVERT: E 262 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7612 (mm110) REVERT: A 168 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7290 (ttm110) REVERT: A 203 ASP cc_start: 0.7856 (m-30) cc_final: 0.7564 (m-30) REVERT: A 334 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8635 (mttp) REVERT: B 64 LYS cc_start: 0.7655 (mttm) cc_final: 0.7455 (mtpt) REVERT: B 71 ARG cc_start: 0.7902 (ptm160) cc_final: 0.7617 (ptm-80) REVERT: B 177 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (p) REVERT: C 64 LYS cc_start: 0.7627 (mttm) cc_final: 0.7388 (mtpt) REVERT: C 165 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7369 (mpt180) REVERT: D 63 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7856 (mt-10) outliers start: 35 outliers final: 19 residues processed: 209 average time/residue: 1.2865 time to fit residues: 296.5565 Evaluate side-chains 201 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN B 308 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN D 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.188 Angle : 0.515 11.907 20980 Z= 0.252 Chirality : 0.038 0.133 2275 Planarity : 0.002 0.023 2625 Dihedral : 3.755 14.547 2055 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.08 % Allowed : 18.87 % Favored : 79.06 % 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: 0.45 (0.19), residues: 1820 helix: 0.97 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.88 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 PHE 0.018 0.001 PHE C 276 TYR 0.017 0.001 TYR C 72 ARG 0.007 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7755 (ttm170) REVERT: A 168 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7293 (ttm110) REVERT: A 175 ASN cc_start: 0.7936 (t0) cc_final: 0.7589 (m-40) REVERT: A 203 ASP cc_start: 0.7859 (m-30) cc_final: 0.7570 (m-30) REVERT: A 334 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8640 (mttp) REVERT: B 71 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7671 (ptm-80) REVERT: B 177 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 64 LYS cc_start: 0.7608 (mttm) cc_final: 0.7368 (mtpt) REVERT: C 77 PRO cc_start: 0.8830 (Cg_exo) cc_final: 0.8592 (Cg_endo) REVERT: C 165 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7356 (mpt180) REVERT: D 63 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7895 (mt-10) outliers start: 33 outliers final: 21 residues processed: 207 average time/residue: 1.3229 time to fit residues: 301.5691 Evaluate side-chains 206 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN B 308 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN D 308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15470 Z= 0.197 Angle : 0.509 11.623 20980 Z= 0.252 Chirality : 0.039 0.129 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.760 15.112 2055 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.14 % Allowed : 18.99 % Favored : 78.87 % 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: 0.50 (0.19), residues: 1820 helix: 1.00 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 PHE 0.018 0.001 PHE A 80 TYR 0.031 0.001 TYR D 68 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7763 (ttm170) REVERT: E 175 ASN cc_start: 0.7939 (t0) cc_final: 0.7651 (m110) REVERT: E 177 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 168 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7286 (ttm110) REVERT: A 175 ASN cc_start: 0.7908 (t0) cc_final: 0.7564 (m-40) REVERT: A 203 ASP cc_start: 0.7863 (m-30) cc_final: 0.7590 (m-30) REVERT: A 334 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8637 (mttp) REVERT: B 71 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7678 (ptm-80) REVERT: B 177 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (p) REVERT: C 25 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8010 (mtp85) REVERT: C 64 LYS cc_start: 0.7643 (mttm) cc_final: 0.7431 (mtpt) REVERT: C 77 PRO cc_start: 0.8874 (Cg_exo) cc_final: 0.8643 (Cg_endo) REVERT: C 165 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7354 (mpt180) REVERT: C 262 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: D 63 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7754 (mt-10) outliers start: 34 outliers final: 20 residues processed: 213 average time/residue: 1.2789 time to fit residues: 299.4048 Evaluate side-chains 212 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.0270 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 0.0270 chunk 110 optimal weight: 0.0570 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN C 308 ASN C 361 GLN D 280 GLN D 361 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15470 Z= 0.125 Angle : 0.490 11.955 20980 Z= 0.240 Chirality : 0.037 0.129 2275 Planarity : 0.002 0.026 2625 Dihedral : 3.681 15.248 2055 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.89 % Allowed : 19.25 % Favored : 78.87 % 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: 0.67 (0.20), residues: 1820 helix: 1.15 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.82 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.004 0.000 HIS C 91 PHE 0.021 0.001 PHE D 282 TYR 0.014 0.001 TYR C 72 ARG 0.007 0.000 ARG C 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: E 175 ASN cc_start: 0.7903 (t0) cc_final: 0.7646 (m110) REVERT: E 177 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8589 (p) REVERT: E 361 GLN cc_start: 0.7654 (mt0) cc_final: 0.7284 (mm-40) REVERT: A 168 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7296 (ttm110) REVERT: A 175 ASN cc_start: 0.7851 (t0) cc_final: 0.7551 (m-40) REVERT: A 203 ASP cc_start: 0.7801 (m-30) cc_final: 0.7529 (m-30) REVERT: A 334 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8639 (mttp) REVERT: B 71 ARG cc_start: 0.7891 (ptm160) cc_final: 0.7678 (ptm-80) REVERT: B 177 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 68 TYR cc_start: 0.7784 (t80) cc_final: 0.7540 (t80) REVERT: C 77 PRO cc_start: 0.8850 (Cg_exo) cc_final: 0.8607 (Cg_endo) REVERT: C 165 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7281 (mpt180) REVERT: C 262 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7783 (mm-40) outliers start: 30 outliers final: 17 residues processed: 225 average time/residue: 1.2804 time to fit residues: 317.1254 Evaluate side-chains 210 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 308 ASN D 361 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108114 restraints weight = 18907.542| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.96 r_work: 0.3219 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.165 Angle : 0.496 11.714 20980 Z= 0.245 Chirality : 0.038 0.128 2275 Planarity : 0.003 0.031 2625 Dihedral : 3.699 15.735 2055 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.82 % Allowed : 19.62 % Favored : 78.55 % 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: 0.68 (0.20), residues: 1820 helix: 1.14 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.78 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.003 0.000 HIS B 91 PHE 0.016 0.001 PHE E 276 TYR 0.028 0.001 TYR D 68 ARG 0.007 0.000 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5391.28 seconds wall clock time: 95 minutes 51.18 seconds (5751.18 seconds total)