Starting phenix.real_space_refine on Sat Mar 16 12:16:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbk_27287/03_2024/8dbk_27287_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.333 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 9052 2.51 5 N 2546 2.21 5 O 2870 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 GLU 39": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "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 GLU 201": "OE1" <-> "OE2" 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 ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 214": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "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 GLU 298": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "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 GLU 298": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "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 GLU 298": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "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 GLU 298": "OE1" <-> "OE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14612 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "B" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} 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: 313 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 301 not shown) Time building chain proxies: 8.29, per 1000 atoms: 0.57 Number of scatterers: 14612 At special positions: 0 Unit cell: (122.396, 128.185, 78.565, 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 2870 8.00 N 2546 7.00 C 9052 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: 6.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 22 sheets defined 36.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 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 172 through 185 removed outlier: 3.601A pdb=" N ALA A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) 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: 3.737A 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 172 through 185 removed outlier: 4.753A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 185 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.646A 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 172 through 185 removed outlier: 3.551A pdb=" N ALA C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.691A 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 172 through 185 removed outlier: 3.552A pdb=" N ALA D 175 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.691A 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 172 through 185 removed outlier: 3.551A pdb=" N ALA E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.690A 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 172 through 185 removed outlier: 3.551A pdb=" N ALA F 175 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.691A 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: 6.268A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.092A 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: 7.845A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 244 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 269 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 246 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL A 271 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 248 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.994A 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: 6.333A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 6.087A 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 204 through 208 removed outlier: 3.755A pdb=" N ASP B 188 " --> pdb=" O CYS B 165 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 215 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 168 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 217 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.134A 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 166 through 169 removed outlier: 6.353A pdb=" N ARG C 243 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 218 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 245 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP C 220 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 247 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 268 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU C 248 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL C 270 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 191 through 194 Processing sheet with id= K, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= M, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG D 243 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU D 218 " --> pdb=" O ARG D 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR D 245 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP D 220 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 247 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA D 268 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 248 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 270 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 191 through 194 Processing sheet with id= O, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.260A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= Q, first strand: chain 'E' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG E 243 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 218 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR E 245 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP E 220 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE E 247 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA E 268 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU E 248 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 270 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 191 through 194 Processing sheet with id= S, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= U, first strand: chain 'F' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG F 243 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU F 218 " --> pdb=" O ARG F 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR F 245 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP F 220 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE F 247 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA F 268 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU F 248 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL F 270 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 191 through 194 509 hydrogen bonds defined for protein. 1266 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: 4.43 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4856 1.34 - 1.46: 2334 1.46 - 1.58: 7431 1.58 - 1.69: 35 1.69 - 1.81: 150 Bond restraints: 14806 Sorted by residual: bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3' ATP A 401 " pdb=" C4' ATP A 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP D 401 " pdb=" C4' ATP D 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ATP F 401 " pdb=" C4' ATP F 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.26e+02 ... (remaining 14801 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.51: 282 105.51 - 112.66: 8306 112.66 - 119.80: 4779 119.80 - 126.95: 6538 126.95 - 134.09: 179 Bond angle restraints: 20084 Sorted by residual: angle pdb=" C1' ATP E 401 " pdb=" N9 ATP E 401 " pdb=" C8 ATP E 401 " ideal model delta sigma weight residual 92.72 126.87 -34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C1' ATP F 401 " pdb=" N9 ATP F 401 " pdb=" C8 ATP F 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP C 401 " pdb=" N9 ATP C 401 " pdb=" C8 ATP C 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP A 401 " pdb=" N9 ATP A 401 " pdb=" C8 ATP A 401 " ideal model delta sigma weight residual 92.72 126.84 -34.12 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP D 401 " pdb=" N9 ATP D 401 " pdb=" C8 ATP D 401 " ideal model delta sigma weight residual 92.72 126.83 -34.11 3.00e+00 1.11e-01 1.29e+02 ... (remaining 20079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 8515 26.90 - 53.80: 446 53.80 - 80.70: 90 80.70 - 107.61: 12 107.61 - 134.51: 15 Dihedral angle restraints: 9078 sinusoidal: 3658 harmonic: 5420 Sorted by residual: dihedral pdb=" CA ASP D 101 " pdb=" C ASP D 101 " pdb=" N LYS D 102 " pdb=" CA LYS D 102 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP F 101 " pdb=" C ASP F 101 " pdb=" N LYS F 102 " pdb=" CA LYS F 102 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP E 101 " pdb=" C ASP E 101 " pdb=" N LYS E 102 " pdb=" CA LYS E 102 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 9075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1579 0.052 - 0.105: 583 0.105 - 0.157: 140 0.157 - 0.210: 18 0.210 - 0.262: 10 Chirality restraints: 2330 Sorted by residual: chirality pdb=" CA ASP B 101 " pdb=" N ASP B 101 " pdb=" C ASP B 101 " pdb=" CB ASP B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASP A 101 " pdb=" N ASP A 101 " pdb=" C ASP A 101 " pdb=" CB ASP A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 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 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2327 not shown) Planarity restraints: 2535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX E 402 " 0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX E 402 " 0.851 2.00e-02 2.50e+03 pdb=" C3 HSX E 402 " -0.039 2.00e-02 2.50e+03 pdb=" C4 HSX E 402 " -0.320 2.00e-02 2.50e+03 pdb=" C5 HSX E 402 " 0.562 2.00e-02 2.50e+03 pdb=" O1 HSX E 402 " -0.780 2.00e-02 2.50e+03 pdb=" O2 HSX E 402 " 0.858 2.00e-02 2.50e+03 pdb=" O3 HSX E 402 " -1.241 2.00e-02 2.50e+03 pdb=" O4 HSX E 402 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX C 402 " -0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX C 402 " -0.851 2.00e-02 2.50e+03 pdb=" C3 HSX C 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX C 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX C 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX C 402 " 0.780 2.00e-02 2.50e+03 pdb=" O2 HSX C 402 " -0.858 2.00e-02 2.50e+03 pdb=" O3 HSX C 402 " 1.241 2.00e-02 2.50e+03 pdb=" O4 HSX C 402 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 402 " 0.274 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX A 402 " 0.851 2.00e-02 2.50e+03 pdb=" C3 HSX A 402 " -0.038 2.00e-02 2.50e+03 pdb=" C4 HSX A 402 " -0.320 2.00e-02 2.50e+03 pdb=" C5 HSX A 402 " 0.562 2.00e-02 2.50e+03 pdb=" O1 HSX A 402 " -0.781 2.00e-02 2.50e+03 pdb=" O2 HSX A 402 " 0.858 2.00e-02 2.50e+03 pdb=" O3 HSX A 402 " -1.241 2.00e-02 2.50e+03 pdb=" O4 HSX A 402 " -0.164 2.00e-02 2.50e+03 ... (remaining 2532 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 81 2.39 - 3.02: 8797 3.02 - 3.64: 22951 3.64 - 4.27: 35939 4.27 - 4.90: 58649 Nonbonded interactions: 126417 Sorted by model distance: nonbonded pdb=" O1B PRP B 401 " pdb="MG MG B 405 " model vdw 1.760 2.170 nonbonded pdb=" O2 PRP B 401 " pdb="MG MG B 405 " model vdw 1.782 2.170 nonbonded pdb=" CE MET D 68 " pdb=" CE MET E 68 " model vdw 1.862 3.880 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 502 " model vdw 1.866 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 501 " model vdw 1.942 2.170 ... (remaining 126412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 195 or resid 203 through 317 or resid 403 throug \ h 405)) selection = (chain 'B' and (resid 2 through 195 or resid 203 through 317 or resid 403 throug \ h 405)) selection = (chain 'C' and (resid 2 through 317 or resid 403 through 405)) selection = (chain 'D' and (resid 2 through 317 or resid 403 through 405)) selection = (chain 'E' and (resid 2 through 317 or resid 403 through 405)) selection = (chain 'F' and (resid 2 through 317 or resid 403 through 405)) } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.450 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.410 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.012 0.235 14806 Z= 0.794 Angle : 1.130 34.146 20084 Z= 0.511 Chirality : 0.057 0.262 2330 Planarity : 0.040 0.678 2535 Dihedral : 18.001 134.507 5546 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 1.07 % Allowed : 12.25 % Favored : 86.68 % Cbeta Deviations : 0.11 % 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: 1848 helix: 1.53 (0.20), residues: 735 sheet: -0.40 (0.24), residues: 492 loop : -0.25 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 162 HIS 0.010 0.002 HIS A 12 PHE 0.018 0.002 PHE D 189 TYR 0.022 0.003 TYR E 146 ARG 0.010 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 331 time to evaluate : 1.611 Fit side-chains REVERT: B 294 MET cc_start: 0.8505 (pmm) cc_final: 0.8291 (pmm) REVERT: C 84 ARG cc_start: 0.8574 (ttt90) cc_final: 0.8193 (ttt90) REVERT: C 127 MET cc_start: 0.8607 (ttm) cc_final: 0.8185 (ttm) REVERT: C 205 MET cc_start: 0.6531 (mmm) cc_final: 0.6198 (mmt) REVERT: D 191 LEU cc_start: 0.6401 (mt) cc_final: 0.5508 (tt) REVERT: E 191 LEU cc_start: 0.7162 (mt) cc_final: 0.6330 (tt) REVERT: E 267 GLU cc_start: 0.7395 (tp30) cc_final: 0.7186 (tp30) REVERT: F 51 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8178 (mm-30) outliers start: 17 outliers final: 4 residues processed: 345 average time/residue: 1.4678 time to fit residues: 548.4354 Evaluate side-chains 289 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 285 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.0020 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 288 GLN B 13 GLN B 38 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 38 GLN D 13 GLN D 17 GLN D 38 GLN D 305 ASN E 13 GLN E 38 GLN F 262 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14806 Z= 0.173 Angle : 1.493 46.742 20084 Z= 0.559 Chirality : 0.047 0.169 2330 Planarity : 0.004 0.114 2535 Dihedral : 15.267 113.434 2162 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 11.49 % Favored : 85.92 % 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: 0.76 (0.20), residues: 1848 helix: 1.74 (0.21), residues: 739 sheet: -0.23 (0.24), residues: 504 loop : -0.25 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 162 HIS 0.007 0.001 HIS A 193 PHE 0.013 0.001 PHE E 189 TYR 0.009 0.001 TYR F 146 ARG 0.005 0.000 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 328 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: B 294 MET cc_start: 0.8579 (pmm) cc_final: 0.8318 (pmm) REVERT: C 127 MET cc_start: 0.8569 (ttm) cc_final: 0.8185 (ttm) REVERT: C 191 LEU cc_start: 0.6807 (mt) cc_final: 0.6123 (tm) REVERT: C 205 MET cc_start: 0.6685 (mmm) cc_final: 0.6180 (mmt) REVERT: E 191 LEU cc_start: 0.6858 (mt) cc_final: 0.6092 (tt) REVERT: E 267 GLU cc_start: 0.7383 (tp30) cc_final: 0.7166 (tp30) REVERT: E 291 ASP cc_start: 0.8677 (t0) cc_final: 0.8339 (t0) REVERT: F 51 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8106 (mm-30) REVERT: F 191 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.5615 (tt) outliers start: 41 outliers final: 23 residues processed: 351 average time/residue: 1.3151 time to fit residues: 503.2646 Evaluate side-chains 325 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 301 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 262 ASN B 288 GLN C 13 GLN C 38 GLN D 17 GLN D 38 GLN E 38 GLN E 262 ASN F 262 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14806 Z= 0.273 Angle : 1.534 46.724 20084 Z= 0.584 Chirality : 0.050 0.205 2330 Planarity : 0.004 0.108 2535 Dihedral : 14.242 106.057 2159 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.90 % Allowed : 11.36 % Favored : 85.73 % 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: 0.64 (0.20), residues: 1848 helix: 1.48 (0.21), residues: 739 sheet: -0.21 (0.24), residues: 494 loop : -0.16 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP F 162 HIS 0.006 0.001 HIS A 193 PHE 0.018 0.002 PHE E 189 TYR 0.012 0.002 TYR A 245 ARG 0.006 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 304 time to evaluate : 1.819 Fit side-chains REVERT: A 248 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 205 MET cc_start: 0.8383 (mtt) cc_final: 0.8057 (mtm) REVERT: B 294 MET cc_start: 0.8620 (pmm) cc_final: 0.8222 (pmm) REVERT: C 127 MET cc_start: 0.8661 (ttm) cc_final: 0.8222 (ttm) REVERT: C 191 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.5973 (tm) REVERT: C 205 MET cc_start: 0.6852 (mmm) cc_final: 0.6342 (mmt) REVERT: D 191 LEU cc_start: 0.6647 (mt) cc_final: 0.5678 (tp) REVERT: D 205 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5181 (mpt) REVERT: E 267 GLU cc_start: 0.7339 (tp30) cc_final: 0.7130 (tp30) REVERT: F 51 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8147 (mm-30) REVERT: F 158 ASN cc_start: 0.8129 (m-40) cc_final: 0.7856 (m110) REVERT: F 163 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7962 (mtt90) REVERT: F 191 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.5921 (tt) outliers start: 46 outliers final: 27 residues processed: 329 average time/residue: 1.4300 time to fit residues: 509.7278 Evaluate side-chains 331 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 300 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 288 GLN C 13 GLN C 38 GLN D 38 GLN E 38 GLN F 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14806 Z= 0.194 Angle : 1.498 46.990 20084 Z= 0.561 Chirality : 0.047 0.175 2330 Planarity : 0.004 0.110 2535 Dihedral : 13.588 97.720 2159 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.53 % Allowed : 11.93 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1848 helix: 1.47 (0.21), residues: 746 sheet: -0.19 (0.24), residues: 504 loop : -0.27 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 162 HIS 0.007 0.001 HIS A 193 PHE 0.014 0.001 PHE E 189 TYR 0.010 0.001 TYR A 245 ARG 0.004 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 312 time to evaluate : 1.808 Fit side-chains REVERT: A 248 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7377 (mp) REVERT: B 205 MET cc_start: 0.8412 (mtt) cc_final: 0.8058 (mtm) REVERT: B 294 MET cc_start: 0.8615 (pmm) cc_final: 0.8281 (pmm) REVERT: C 127 MET cc_start: 0.8632 (ttm) cc_final: 0.8115 (ttm) REVERT: C 191 LEU cc_start: 0.6894 (mt) cc_final: 0.6057 (tm) REVERT: C 205 MET cc_start: 0.6694 (mmm) cc_final: 0.6190 (mmt) REVERT: D 191 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5649 (tp) REVERT: D 205 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5173 (mpt) REVERT: E 267 GLU cc_start: 0.7360 (tp30) cc_final: 0.7140 (tp30) REVERT: F 51 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8098 (mm-30) REVERT: F 191 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.5846 (tt) outliers start: 40 outliers final: 20 residues processed: 335 average time/residue: 1.3872 time to fit residues: 505.1427 Evaluate side-chains 327 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 303 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 178 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 183 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 263 ASN A 288 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 38 GLN D 38 GLN E 38 GLN F 12 HIS F 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14806 Z= 0.305 Angle : 1.540 46.711 20084 Z= 0.588 Chirality : 0.051 0.221 2330 Planarity : 0.005 0.108 2535 Dihedral : 13.707 102.933 2157 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.97 % Allowed : 11.74 % Favored : 85.29 % 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: 0.52 (0.20), residues: 1848 helix: 1.33 (0.21), residues: 743 sheet: -0.21 (0.24), residues: 494 loop : -0.22 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 162 HIS 0.006 0.001 HIS A 193 PHE 0.016 0.002 PHE D 189 TYR 0.014 0.002 TYR A 245 ARG 0.007 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 295 time to evaluate : 1.797 Fit side-chains REVERT: A 248 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7436 (mp) REVERT: B 294 MET cc_start: 0.8643 (pmm) cc_final: 0.8316 (pmm) REVERT: C 205 MET cc_start: 0.6867 (mmm) cc_final: 0.6280 (mmt) REVERT: D 191 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.5699 (tp) REVERT: D 205 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5165 (mpt) REVERT: E 207 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7104 (tp) REVERT: E 267 GLU cc_start: 0.7355 (tp30) cc_final: 0.7142 (tp30) REVERT: F 51 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8081 (mm-30) REVERT: F 191 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6081 (tt) outliers start: 47 outliers final: 28 residues processed: 326 average time/residue: 1.3851 time to fit residues: 490.7882 Evaluate side-chains 330 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 297 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 176 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN C 13 GLN C 38 GLN D 38 GLN D 288 GLN E 38 GLN F 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14806 Z= 0.178 Angle : 1.491 47.081 20084 Z= 0.557 Chirality : 0.047 0.173 2330 Planarity : 0.004 0.110 2535 Dihedral : 12.868 95.686 2157 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.15 % Allowed : 12.31 % Favored : 85.54 % 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: 0.61 (0.20), residues: 1848 helix: 1.47 (0.21), residues: 746 sheet: -0.18 (0.24), residues: 504 loop : -0.26 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 162 HIS 0.007 0.001 HIS A 193 PHE 0.021 0.001 PHE E 189 TYR 0.011 0.001 TYR B 146 ARG 0.007 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 302 time to evaluate : 1.802 Fit side-chains REVERT: A 248 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7352 (mp) REVERT: B 205 MET cc_start: 0.8410 (mtt) cc_final: 0.8053 (mtm) REVERT: B 294 MET cc_start: 0.8606 (pmm) cc_final: 0.8308 (pmm) REVERT: C 191 LEU cc_start: 0.6904 (mt) cc_final: 0.6075 (tm) REVERT: C 205 MET cc_start: 0.6744 (mmm) cc_final: 0.6242 (mmt) REVERT: D 205 MET cc_start: 0.5960 (OUTLIER) cc_final: 0.5125 (mpt) REVERT: E 191 LEU cc_start: 0.6840 (mt) cc_final: 0.6023 (tt) REVERT: E 207 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6978 (tp) REVERT: E 267 GLU cc_start: 0.7339 (tp30) cc_final: 0.7107 (tp30) REVERT: F 51 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8059 (mm-30) REVERT: F 191 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.5835 (tt) REVERT: F 294 MET cc_start: 0.8594 (pmm) cc_final: 0.8384 (pmm) outliers start: 34 outliers final: 21 residues processed: 321 average time/residue: 1.4749 time to fit residues: 512.9525 Evaluate side-chains 324 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 299 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 288 GLN C 13 GLN C 38 GLN D 38 GLN D 288 GLN E 38 GLN E 262 ASN F 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14806 Z= 0.220 Angle : 1.507 46.931 20084 Z= 0.567 Chirality : 0.048 0.207 2330 Planarity : 0.004 0.109 2535 Dihedral : 12.659 93.528 2157 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 12.06 % Favored : 85.23 % 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: 0.53 (0.20), residues: 1848 helix: 1.37 (0.21), residues: 750 sheet: -0.20 (0.24), residues: 504 loop : -0.28 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 162 HIS 0.007 0.001 HIS A 193 PHE 0.024 0.001 PHE E 189 TYR 0.014 0.002 TYR A 245 ARG 0.008 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 1.785 Fit side-chains REVERT: A 248 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7379 (mp) REVERT: B 205 MET cc_start: 0.8407 (mtt) cc_final: 0.8050 (mtm) REVERT: B 294 MET cc_start: 0.8616 (pmm) cc_final: 0.8321 (pmm) REVERT: C 191 LEU cc_start: 0.6937 (mt) cc_final: 0.6070 (tm) REVERT: C 205 MET cc_start: 0.6746 (mmm) cc_final: 0.6251 (mmt) REVERT: D 191 LEU cc_start: 0.6380 (mt) cc_final: 0.5556 (tp) REVERT: D 205 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5111 (mpt) REVERT: E 191 LEU cc_start: 0.6924 (mt) cc_final: 0.6054 (tt) REVERT: E 207 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6993 (tp) REVERT: E 267 GLU cc_start: 0.7318 (tp30) cc_final: 0.7076 (tp30) REVERT: F 51 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8041 (mm-30) REVERT: F 191 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5858 (tt) outliers start: 43 outliers final: 29 residues processed: 326 average time/residue: 1.4309 time to fit residues: 506.7618 Evaluate side-chains 328 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 295 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 288 GLN C 13 GLN C 38 GLN D 38 GLN D 288 GLN E 38 GLN E 262 ASN F 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14806 Z= 0.185 Angle : 1.491 46.990 20084 Z= 0.557 Chirality : 0.047 0.188 2330 Planarity : 0.004 0.110 2535 Dihedral : 12.188 90.399 2157 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.34 % Allowed : 12.63 % Favored : 85.04 % 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: 0.59 (0.20), residues: 1848 helix: 1.45 (0.21), residues: 750 sheet: -0.17 (0.24), residues: 504 loop : -0.31 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 162 HIS 0.007 0.001 HIS A 193 PHE 0.022 0.001 PHE E 189 TYR 0.012 0.001 TYR B 146 ARG 0.008 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 299 time to evaluate : 1.734 Fit side-chains REVERT: A 248 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7351 (mp) REVERT: B 205 MET cc_start: 0.8422 (mtt) cc_final: 0.8059 (mtm) REVERT: B 294 MET cc_start: 0.8606 (pmm) cc_final: 0.8301 (pmm) REVERT: C 191 LEU cc_start: 0.6857 (mt) cc_final: 0.6066 (tm) REVERT: C 205 MET cc_start: 0.6752 (mmm) cc_final: 0.6195 (mmt) REVERT: D 205 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5535 (mmt) REVERT: E 191 LEU cc_start: 0.6898 (mt) cc_final: 0.6077 (tt) REVERT: E 207 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6906 (tp) REVERT: E 267 GLU cc_start: 0.7354 (tp30) cc_final: 0.7101 (tp30) REVERT: F 51 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8034 (mm-30) REVERT: F 191 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.5774 (tt) REVERT: F 294 MET cc_start: 0.8631 (pmm) cc_final: 0.8321 (pmm) outliers start: 37 outliers final: 26 residues processed: 320 average time/residue: 1.4341 time to fit residues: 498.0364 Evaluate side-chains 326 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 296 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 288 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 38 GLN C 158 ASN D 38 GLN D 288 GLN D 305 ASN E 38 GLN F 262 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14806 Z= 0.389 Angle : 1.565 46.473 20084 Z= 0.604 Chirality : 0.054 0.286 2330 Planarity : 0.005 0.106 2535 Dihedral : 13.068 98.960 2157 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.46 % Allowed : 12.44 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1848 helix: 1.23 (0.20), residues: 744 sheet: -0.22 (0.24), residues: 494 loop : -0.23 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP F 162 HIS 0.009 0.002 HIS A 12 PHE 0.029 0.002 PHE E 189 TYR 0.020 0.003 TYR B 146 ARG 0.007 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 296 time to evaluate : 1.625 Fit side-chains REVERT: A 248 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 294 MET cc_start: 0.8645 (pmm) cc_final: 0.8310 (pmm) REVERT: C 205 MET cc_start: 0.6739 (mmm) cc_final: 0.6281 (mmt) REVERT: D 191 LEU cc_start: 0.6584 (mt) cc_final: 0.5888 (tt) REVERT: D 205 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5190 (mpt) REVERT: E 207 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7113 (tp) REVERT: E 267 GLU cc_start: 0.7352 (tp30) cc_final: 0.7118 (tp30) REVERT: F 51 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8040 (mm-30) REVERT: F 191 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6121 (tt) outliers start: 39 outliers final: 26 residues processed: 319 average time/residue: 1.5018 time to fit residues: 518.6221 Evaluate side-chains 324 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 294 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 262 ASN C 13 GLN C 38 GLN C 158 ASN D 38 GLN D 288 GLN E 38 GLN E 262 ASN F 262 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14806 Z= 0.224 Angle : 1.509 46.885 20084 Z= 0.569 Chirality : 0.048 0.234 2330 Planarity : 0.004 0.110 2535 Dihedral : 12.448 93.440 2157 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.83 % Allowed : 13.51 % Favored : 84.66 % 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: 0.49 (0.20), residues: 1848 helix: 1.32 (0.21), residues: 750 sheet: -0.23 (0.24), residues: 504 loop : -0.28 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 162 HIS 0.007 0.001 HIS A 193 PHE 0.026 0.002 PHE E 189 TYR 0.017 0.002 TYR B 146 ARG 0.008 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 1.381 Fit side-chains REVERT: A 248 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7362 (mp) REVERT: B 294 MET cc_start: 0.8621 (pmm) cc_final: 0.8331 (pmm) REVERT: C 191 LEU cc_start: 0.6892 (mt) cc_final: 0.6067 (tm) REVERT: C 205 MET cc_start: 0.6735 (mmm) cc_final: 0.6229 (mmt) REVERT: D 191 LEU cc_start: 0.6390 (mt) cc_final: 0.5638 (tp) REVERT: D 205 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5160 (mpt) REVERT: E 115 MET cc_start: 0.8751 (mtm) cc_final: 0.8401 (mtp) REVERT: E 191 LEU cc_start: 0.7021 (mt) cc_final: 0.6116 (tt) REVERT: E 207 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6936 (tp) REVERT: E 267 GLU cc_start: 0.7323 (tp30) cc_final: 0.7090 (tp30) REVERT: F 51 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 191 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.5929 (tt) outliers start: 29 outliers final: 20 residues processed: 313 average time/residue: 1.4371 time to fit residues: 487.5621 Evaluate side-chains 318 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 144 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 288 GLN C 13 GLN C 38 GLN D 38 GLN D 288 GLN E 38 GLN E 262 ASN F 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121435 restraints weight = 12387.292| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.08 r_work: 0.3255 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 297 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14806 Z= 0.223 Angle : 1.511 46.876 20084 Z= 0.570 Chirality : 0.048 0.231 2330 Planarity : 0.004 0.109 2535 Dihedral : 12.243 91.668 2157 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.96 % Allowed : 13.51 % Favored : 84.53 % 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: 0.49 (0.20), residues: 1848 helix: 1.33 (0.21), residues: 751 sheet: -0.24 (0.24), residues: 504 loop : -0.29 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 162 HIS 0.006 0.001 HIS A 193 PHE 0.030 0.002 PHE E 189 TYR 0.017 0.002 TYR B 146 ARG 0.008 0.000 ARG D 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7589.75 seconds wall clock time: 133 minutes 41.88 seconds (8021.88 seconds total)