Starting phenix.real_space_refine on Fri Feb 16 05:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/02_2024/8dbg_27283_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/02_2024/8dbg_27283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/02_2024/8dbg_27283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/02_2024/8dbg_27283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/02_2024/8dbg_27283_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/02_2024/8dbg_27283_updated.pdb" } resolution = 2.2 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= 0.300 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 P 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8952 2.51 5 N 2520 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 306 not shown) Time building chain proxies: 7.89, per 1000 atoms: 0.55 Number of scatterers: 14442 At special positions: 0 Unit cell: (122.396, 129.839, 76.911, 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) S 102 16.00 P 30 15.00 Mg 12 11.99 O 2826 8.00 N 2520 7.00 C 8952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 18 sheets defined 36.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.667A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.667A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.668A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.668A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.668A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 310 through 313 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.668A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 310 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4701 1.33 - 1.45: 1661 1.45 - 1.57: 8086 1.57 - 1.69: 30 1.69 - 1.81: 150 Bond restraints: 14628 Sorted by residual: bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O2 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O2 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14623 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.76: 420 106.76 - 113.59: 8589 113.59 - 120.42: 5258 120.42 - 127.25: 5413 127.25 - 134.08: 156 Bond angle restraints: 19836 Sorted by residual: angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 132.36 7.51 1.00e+00 1.00e+00 5.65e+01 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.60e+01 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 132.40 7.47 1.00e+00 1.00e+00 5.58e+01 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 132.40 7.47 1.00e+00 1.00e+00 5.58e+01 ... (remaining 19831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8016 17.95 - 35.90: 678 35.90 - 53.84: 216 53.84 - 71.79: 67 71.79 - 89.74: 47 Dihedral angle restraints: 9024 sinusoidal: 3648 harmonic: 5376 Sorted by residual: dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1304 0.040 - 0.079: 716 0.079 - 0.119: 247 0.119 - 0.158: 43 0.158 - 0.198: 24 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CG LEU D 248 " pdb=" CB LEU D 248 " pdb=" CD1 LEU D 248 " pdb=" CD2 LEU D 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU E 248 " pdb=" CB LEU E 248 " pdb=" CD1 LEU E 248 " pdb=" CD2 LEU E 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CG LEU B 248 " pdb=" CB LEU B 248 " pdb=" CD1 LEU B 248 " pdb=" CD2 LEU B 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 2331 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 180 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C SER F 180 " 0.029 2.00e-02 2.50e+03 pdb=" O SER F 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE F 181 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C SER A 180 " -0.029 2.00e-02 2.50e+03 pdb=" O SER A 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 181 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 180 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C SER C 180 " -0.029 2.00e-02 2.50e+03 pdb=" O SER C 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 181 " 0.010 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 114 2.55 - 3.13: 11709 3.13 - 3.72: 23859 3.72 - 4.31: 33767 4.31 - 4.90: 55541 Nonbonded interactions: 124990 Sorted by model distance: nonbonded pdb="MG MG D 404 " pdb=" O HOH D 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 501 " model vdw 1.959 2.170 ... (remaining 124985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.01 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 7.390 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 41.010 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.007 0.070 14628 Z= 0.456 Angle : 0.693 7.513 19836 Z= 0.437 Chirality : 0.054 0.198 2334 Planarity : 0.003 0.019 2502 Dihedral : 17.531 89.739 5520 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.97 % Allowed : 12.53 % Favored : 85.50 % 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: 0.54 (0.20), residues: 1830 helix: 1.27 (0.20), residues: 744 sheet: 0.06 (0.25), residues: 474 loop : -0.38 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 162 HIS 0.005 0.001 HIS E 130 PHE 0.011 0.002 PHE D 189 TYR 0.022 0.004 TYR D 146 ARG 0.004 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 339 time to evaluate : 1.672 Fit side-chains REVERT: A 6 ILE cc_start: 0.9058 (mm) cc_final: 0.8813 (mm) REVERT: A 294 MET cc_start: 0.8704 (pmm) cc_final: 0.8435 (pmm) REVERT: C 127 MET cc_start: 0.8754 (ttm) cc_final: 0.8254 (ttm) REVERT: D 127 MET cc_start: 0.8752 (ttm) cc_final: 0.8256 (ttm) REVERT: F 6 ILE cc_start: 0.9058 (mm) cc_final: 0.8811 (mm) REVERT: F 294 MET cc_start: 0.8718 (pmm) cc_final: 0.8453 (pmm) outliers start: 31 outliers final: 24 residues processed: 362 average time/residue: 1.2314 time to fit residues: 488.6926 Evaluate side-chains 306 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 282 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 305 ASN C 38 GLN C 135 GLN C 305 ASN D 38 GLN D 135 GLN D 305 ASN E 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14628 Z= 0.165 Angle : 0.469 4.510 19836 Z= 0.262 Chirality : 0.047 0.165 2334 Planarity : 0.002 0.021 2502 Dihedral : 12.911 86.203 2196 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 12.15 % Favored : 85.24 % 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: 0.92 (0.20), residues: 1830 helix: 1.81 (0.20), residues: 738 sheet: 0.07 (0.25), residues: 468 loop : -0.30 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 162 HIS 0.003 0.001 HIS C 304 PHE 0.010 0.001 PHE F 138 TYR 0.012 0.002 TYR C 146 ARG 0.003 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 307 time to evaluate : 1.925 Fit side-chains REVERT: A 6 ILE cc_start: 0.9011 (mm) cc_final: 0.8740 (mm) REVERT: A 21 ASP cc_start: 0.8137 (m-30) cc_final: 0.7930 (m-30) REVERT: B 6 ILE cc_start: 0.9023 (mm) cc_final: 0.8792 (mm) REVERT: C 127 MET cc_start: 0.8752 (ttm) cc_final: 0.8227 (ttm) REVERT: D 127 MET cc_start: 0.8755 (ttm) cc_final: 0.8223 (ttm) REVERT: E 6 ILE cc_start: 0.9021 (mm) cc_final: 0.8785 (mm) REVERT: F 6 ILE cc_start: 0.9014 (mm) cc_final: 0.8741 (mm) outliers start: 41 outliers final: 24 residues processed: 341 average time/residue: 1.2811 time to fit residues: 477.6172 Evaluate side-chains 325 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 301 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14628 Z= 0.336 Angle : 0.568 5.215 19836 Z= 0.317 Chirality : 0.052 0.205 2334 Planarity : 0.003 0.023 2502 Dihedral : 13.299 85.976 2180 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.16 % Allowed : 11.96 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1830 helix: 1.64 (0.20), residues: 744 sheet: 0.04 (0.25), residues: 468 loop : -0.20 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 162 HIS 0.006 0.002 HIS B 130 PHE 0.010 0.002 PHE B 189 TYR 0.017 0.003 TYR D 146 ARG 0.004 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 311 time to evaluate : 1.688 Fit side-chains REVERT: A 6 ILE cc_start: 0.9078 (mm) cc_final: 0.8846 (mm) REVERT: A 39 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8719 (mt-10) REVERT: F 6 ILE cc_start: 0.9081 (mm) cc_final: 0.8852 (mm) REVERT: F 39 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8714 (mt-10) outliers start: 34 outliers final: 22 residues processed: 339 average time/residue: 1.4172 time to fit residues: 522.6277 Evaluate side-chains 334 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 312 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 0.0030 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14628 Z= 0.139 Angle : 0.446 4.540 19836 Z= 0.248 Chirality : 0.046 0.163 2334 Planarity : 0.002 0.025 2502 Dihedral : 11.467 84.346 2180 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.16 % Allowed : 11.64 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1830 helix: 1.98 (0.20), residues: 738 sheet: 0.08 (0.25), residues: 468 loop : -0.33 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 162 HIS 0.003 0.001 HIS D 304 PHE 0.008 0.001 PHE A 138 TYR 0.010 0.001 TYR D 146 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 324 time to evaluate : 1.698 Fit side-chains REVERT: A 6 ILE cc_start: 0.9038 (mm) cc_final: 0.8766 (mm) REVERT: A 21 ASP cc_start: 0.8193 (m-30) cc_final: 0.7866 (m-30) REVERT: A 39 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 237 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7812 (tp) REVERT: D 237 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7838 (tp) REVERT: D 260 ARG cc_start: 0.8541 (mtt180) cc_final: 0.8185 (mtt180) REVERT: F 6 ILE cc_start: 0.9043 (mm) cc_final: 0.8771 (mm) REVERT: F 39 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8640 (mt-10) outliers start: 34 outliers final: 21 residues processed: 354 average time/residue: 1.3784 time to fit residues: 531.0868 Evaluate side-chains 336 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14628 Z= 0.300 Angle : 0.538 4.825 19836 Z= 0.301 Chirality : 0.051 0.230 2334 Planarity : 0.003 0.023 2502 Dihedral : 12.493 89.554 2176 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.23 % Allowed : 11.83 % Favored : 85.94 % 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: 0.92 (0.20), residues: 1830 helix: 1.77 (0.20), residues: 744 sheet: 0.05 (0.25), residues: 468 loop : -0.24 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 162 HIS 0.005 0.001 HIS B 130 PHE 0.009 0.002 PHE E 189 TYR 0.017 0.002 TYR D 146 ARG 0.004 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 326 time to evaluate : 1.472 Fit side-chains REVERT: A 6 ILE cc_start: 0.9080 (mm) cc_final: 0.8852 (mm) REVERT: A 39 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8733 (mt-10) REVERT: B 6 ILE cc_start: 0.9080 (mm) cc_final: 0.8878 (mm) REVERT: C 243 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6887 (mtm-85) REVERT: C 260 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8209 (mtt180) REVERT: E 6 ILE cc_start: 0.9078 (mm) cc_final: 0.8873 (mm) REVERT: F 6 ILE cc_start: 0.9086 (mm) cc_final: 0.8859 (mm) REVERT: F 39 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8731 (mt-10) REVERT: F 263 ASN cc_start: 0.8090 (m-40) cc_final: 0.7865 (m110) outliers start: 35 outliers final: 22 residues processed: 352 average time/residue: 1.4141 time to fit residues: 539.5241 Evaluate side-chains 345 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 322 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14628 Z= 0.167 Angle : 0.462 4.746 19836 Z= 0.258 Chirality : 0.047 0.179 2334 Planarity : 0.002 0.022 2502 Dihedral : 11.544 86.561 2176 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.23 % Allowed : 11.96 % Favored : 85.81 % 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: 1.03 (0.20), residues: 1830 helix: 1.92 (0.20), residues: 744 sheet: 0.09 (0.25), residues: 468 loop : -0.28 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS D 304 PHE 0.008 0.001 PHE A 138 TYR 0.014 0.002 TYR A 146 ARG 0.002 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 321 time to evaluate : 1.632 Fit side-chains REVERT: A 6 ILE cc_start: 0.9068 (mm) cc_final: 0.8798 (mm) REVERT: A 39 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8667 (mt-10) REVERT: B 6 ILE cc_start: 0.9039 (mm) cc_final: 0.8820 (mm) REVERT: C 237 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7785 (tp) REVERT: C 260 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8193 (mtt180) REVERT: D 237 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7809 (tp) REVERT: E 6 ILE cc_start: 0.9039 (mm) cc_final: 0.8817 (mm) REVERT: F 6 ILE cc_start: 0.9071 (mm) cc_final: 0.8800 (mm) REVERT: F 39 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8666 (mt-10) outliers start: 35 outliers final: 28 residues processed: 352 average time/residue: 1.4106 time to fit residues: 539.9348 Evaluate side-chains 349 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 319 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14628 Z= 0.189 Angle : 0.474 4.867 19836 Z= 0.265 Chirality : 0.047 0.203 2334 Planarity : 0.002 0.021 2502 Dihedral : 11.536 87.176 2176 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.10 % Allowed : 12.66 % Favored : 85.24 % 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: 1.02 (0.20), residues: 1830 helix: 1.92 (0.20), residues: 744 sheet: 0.09 (0.25), residues: 468 loop : -0.30 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 162 HIS 0.003 0.001 HIS E 130 PHE 0.008 0.001 PHE A 138 TYR 0.015 0.002 TYR D 146 ARG 0.003 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 323 time to evaluate : 1.577 Fit side-chains REVERT: A 6 ILE cc_start: 0.9071 (mm) cc_final: 0.8802 (mm) REVERT: A 39 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8680 (mt-10) REVERT: B 6 ILE cc_start: 0.9079 (mm) cc_final: 0.8855 (mm) REVERT: C 237 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7775 (tp) REVERT: D 237 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7803 (tp) REVERT: D 243 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6934 (mtm-85) REVERT: E 6 ILE cc_start: 0.9080 (mm) cc_final: 0.8855 (mm) REVERT: E 153 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8052 (tttp) REVERT: F 6 ILE cc_start: 0.9074 (mm) cc_final: 0.8825 (mm) REVERT: F 39 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8679 (mt-10) outliers start: 33 outliers final: 26 residues processed: 351 average time/residue: 1.3864 time to fit residues: 529.0888 Evaluate side-chains 351 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 321 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 0.0000 chunk 16 optimal weight: 0.4980 chunk 136 optimal weight: 0.5980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14628 Z= 0.130 Angle : 0.432 4.980 19836 Z= 0.240 Chirality : 0.046 0.160 2334 Planarity : 0.002 0.021 2502 Dihedral : 10.632 78.782 2176 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 12.66 % Favored : 85.31 % 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: 1.13 (0.20), residues: 1830 helix: 2.14 (0.20), residues: 738 sheet: 0.13 (0.25), residues: 468 loop : -0.38 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 162 HIS 0.002 0.001 HIS C 304 PHE 0.007 0.001 PHE A 138 TYR 0.012 0.001 TYR A 146 ARG 0.001 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 321 time to evaluate : 1.600 Fit side-chains REVERT: A 6 ILE cc_start: 0.9041 (mm) cc_final: 0.8751 (mm) REVERT: A 39 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8652 (mt-10) REVERT: B 6 ILE cc_start: 0.9024 (mm) cc_final: 0.8795 (mm) REVERT: C 237 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7803 (tp) REVERT: D 237 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7852 (tp) REVERT: E 6 ILE cc_start: 0.9023 (mm) cc_final: 0.8792 (mm) REVERT: F 6 ILE cc_start: 0.9045 (mm) cc_final: 0.8776 (mm) REVERT: F 39 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8631 (mt-10) outliers start: 32 outliers final: 23 residues processed: 349 average time/residue: 1.3927 time to fit residues: 527.7669 Evaluate side-chains 346 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 321 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 0.0270 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.0670 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14628 Z= 0.126 Angle : 0.427 5.010 19836 Z= 0.236 Chirality : 0.046 0.160 2334 Planarity : 0.002 0.020 2502 Dihedral : 10.236 73.958 2176 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.84 % Allowed : 13.30 % Favored : 84.86 % 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: 1.19 (0.20), residues: 1830 helix: 2.14 (0.20), residues: 744 sheet: 0.18 (0.25), residues: 468 loop : -0.33 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 162 HIS 0.002 0.001 HIS D 304 PHE 0.007 0.001 PHE A 138 TYR 0.011 0.001 TYR D 146 ARG 0.001 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 320 time to evaluate : 1.667 Fit side-chains REVERT: A 6 ILE cc_start: 0.9035 (mm) cc_final: 0.8746 (mm) REVERT: A 39 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8660 (mt-10) REVERT: B 6 ILE cc_start: 0.9036 (mm) cc_final: 0.8799 (mm) REVERT: C 237 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7838 (tp) REVERT: D 237 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7862 (tp) REVERT: D 260 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8256 (mtt180) REVERT: E 6 ILE cc_start: 0.9030 (mm) cc_final: 0.8789 (mm) REVERT: F 6 ILE cc_start: 0.9041 (mm) cc_final: 0.8749 (mm) REVERT: F 39 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8647 (mt-10) outliers start: 29 outliers final: 23 residues processed: 345 average time/residue: 1.3790 time to fit residues: 517.6843 Evaluate side-chains 328 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 303 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 263 ASN C 288 GLN D 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14628 Z= 0.227 Angle : 0.496 5.096 19836 Z= 0.277 Chirality : 0.049 0.220 2334 Planarity : 0.003 0.021 2502 Dihedral : 11.160 83.965 2176 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.78 % Allowed : 13.93 % Favored : 84.29 % 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: 1.11 (0.20), residues: 1830 helix: 2.00 (0.20), residues: 744 sheet: 0.15 (0.25), residues: 468 loop : -0.25 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 154 HIS 0.003 0.001 HIS E 130 PHE 0.009 0.001 PHE A 138 TYR 0.019 0.002 TYR A 146 ARG 0.004 0.000 ARG F 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 318 time to evaluate : 1.771 Fit side-chains REVERT: A 6 ILE cc_start: 0.9077 (mm) cc_final: 0.8833 (mm) REVERT: A 39 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8730 (mt-10) REVERT: B 6 ILE cc_start: 0.9079 (mm) cc_final: 0.8854 (mm) REVERT: C 237 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7848 (tp) REVERT: D 237 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7779 (tp) REVERT: E 6 ILE cc_start: 0.9084 (mm) cc_final: 0.8852 (mm) REVERT: F 6 ILE cc_start: 0.9080 (mm) cc_final: 0.8836 (mm) REVERT: F 39 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8722 (mt-10) outliers start: 28 outliers final: 20 residues processed: 340 average time/residue: 1.4517 time to fit residues: 534.9048 Evaluate side-chains 338 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 316 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0170 chunk 43 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 288 GLN D 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117965 restraints weight = 12265.406| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.04 r_work: 0.3154 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14628 Z= 0.243 Angle : 0.509 5.290 19836 Z= 0.284 Chirality : 0.049 0.231 2334 Planarity : 0.003 0.025 2502 Dihedral : 11.661 89.435 2176 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.59 % Allowed : 13.93 % Favored : 84.48 % 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: 1.03 (0.20), residues: 1830 helix: 1.89 (0.20), residues: 744 sheet: 0.13 (0.25), residues: 468 loop : -0.27 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 154 HIS 0.004 0.001 HIS B 130 PHE 0.009 0.001 PHE A 138 TYR 0.020 0.002 TYR A 146 ARG 0.003 0.000 ARG F 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7666.43 seconds wall clock time: 135 minutes 50.36 seconds (8150.36 seconds total)