Starting phenix.real_space_refine on Tue Aug 6 09:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbd_37421/08_2024/8wbd_37421_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbd_37421/08_2024/8wbd_37421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbd_37421/08_2024/8wbd_37421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbd_37421/08_2024/8wbd_37421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbd_37421/08_2024/8wbd_37421_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbd_37421/08_2024/8wbd_37421_neut.cif" } resolution = 2.9 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= 0.003 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 10218 2.51 5 N 2769 2.21 5 O 3044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16157 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2596 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "a" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "c" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'TGL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.93, per 1000 atoms: 0.68 Number of scatterers: 16157 At special positions: 0 Unit cell: (124.1, 126.65, 120.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3044 8.00 N 2769 7.00 C 10218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 15 " distance=2.03 Simple disulfide: pdb=" SG CYS c 55 " - pdb=" SG CYS c 143 " distance=2.03 Simple disulfide: pdb=" SG CYS c 179 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 280 " - pdb=" SG CYS c 329 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 3.0 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 17.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.550A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.575A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.566A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.736A pdb=" N LEU A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.701A pdb=" N ASP B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.786A pdb=" N ASN B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.629A pdb=" N LEU B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.632A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.523A pdb=" N ALA B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.516A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'C' and resid 40 through 53 removed outlier: 4.256A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 82 removed outlier: 3.689A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.670A pdb=" N THR C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.622A pdb=" N LEU C 270 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 271 " --> pdb=" O TRP C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 271' Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 3.565A pdb=" N ASN a 65 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN a 73 " --> pdb=" O LYS a 69 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU a 74 " --> pdb=" O GLN a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.698A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.635A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.637A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.770A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 271' Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.738A pdb=" N MET a 345 " --> pdb=" O GLU a 342 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 51 Processing helix chain 'b' and resid 61 through 72 removed outlier: 3.680A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 83 removed outlier: 3.567A pdb=" N GLY b 83 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 148 removed outlier: 3.704A pdb=" N ARG b 148 " --> pdb=" O ASN b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 183 Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.581A pdb=" N THR b 230 " --> pdb=" O LYS b 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'c' and resid 38 through 53 removed outlier: 3.617A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 82 removed outlier: 3.937A pdb=" N ILE c 66 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET c 67 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASN c 73 " --> pdb=" O LYS c 69 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU c 74 " --> pdb=" O GLN c 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY c 82 " --> pdb=" O VAL c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 148 removed outlier: 3.539A pdb=" N ARG c 147 " --> pdb=" O PRO c 144 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG c 148 " --> pdb=" O ASN c 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 144 through 148' Processing helix chain 'c' and resid 180 through 183 removed outlier: 3.840A pdb=" N LEU c 183 " --> pdb=" O ASP c 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 183' Processing helix chain 'c' and resid 226 through 230 removed outlier: 3.693A pdb=" N THR c 230 " --> pdb=" O LYS c 227 " (cutoff:3.500A) Processing helix chain 'c' and resid 244 through 248 removed outlier: 3.614A pdb=" N ALA c 248 " --> pdb=" O LYS c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 271 removed outlier: 3.829A pdb=" N LEU c 270 " --> pdb=" O PRO c 267 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY c 271 " --> pdb=" O TRP c 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 267 through 271' Processing helix chain 'c' and resid 341 through 345 removed outlier: 3.501A pdb=" N ASN c 344 " --> pdb=" O LYS c 341 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET c 345 " --> pdb=" O GLU c 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 341 through 345' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.222A pdb=" N LYS A 33 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN A 35 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE A 171 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 7.081A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.578A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 212 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 200 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER a 205 " --> pdb=" O ILE a 212 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE a 212 " --> pdb=" O SER a 205 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.031A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.582A pdb=" N GLN B 35 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N PHE B 171 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 removed outlier: 7.034A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 4.778A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE b 212 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU b 274 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.489A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 298 through 302 removed outlier: 5.584A pdb=" N VAL B 346 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 16 removed outlier: 3.554A pdb=" N THR C 2 " --> pdb=" O VAL c 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.747A pdb=" N ASN C 166 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR C 158 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP C 168 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.098A pdb=" N VAL C 89 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 57 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 330 through 331 removed outlier: 4.547A pdb=" N PHE C 277 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLU C 213 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 212 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER C 205 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 214 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS c 214 " --> pdb=" O GLU c 203 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER c 205 " --> pdb=" O ILE c 212 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE c 212 " --> pdb=" O SER c 205 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU c 213 " --> pdb=" O PHE c 277 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE c 277 " --> pdb=" O GLU c 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.202A pdb=" N THR C 286 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 33 through 35 removed outlier: 6.592A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.910A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.101A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 32 through 35 removed outlier: 6.366A pdb=" N LYS b 33 " --> pdb=" O ILE b 167 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET b 169 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN b 35 " --> pdb=" O MET b 169 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN b 166 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR b 158 " --> pdb=" O ASN b 166 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.958A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.241A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 33 through 35 removed outlier: 6.952A pdb=" N TRP c 168 " --> pdb=" O GLU c 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 89 through 90 removed outlier: 6.366A pdb=" N VAL c 89 " --> pdb=" O ILE c 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 284 through 287 419 hydrogen bonds defined for protein. 1104 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: 4.89 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2691 1.31 - 1.44: 4592 1.44 - 1.57: 9113 1.57 - 1.69: 0 1.69 - 1.82: 180 Bond restraints: 16576 Sorted by residual: bond pdb=" CA ASN b 207 " pdb=" C ASN b 207 " ideal model delta sigma weight residual 1.531 1.468 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" OG3 TGL b 401 " pdb=" CC1 TGL b 401 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" OG1 TGL b 401 " pdb=" CA1 TGL b 401 " ideal model delta sigma weight residual 1.332 1.397 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CB1 TGL b 401 " pdb=" OG2 TGL b 401 " ideal model delta sigma weight residual 1.335 1.399 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 16571 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.99: 580 106.99 - 113.76: 9135 113.76 - 120.54: 5878 120.54 - 127.32: 6577 127.32 - 134.09: 297 Bond angle restraints: 22467 Sorted by residual: angle pdb=" N VAL C 25 " pdb=" CA VAL C 25 " pdb=" C VAL C 25 " ideal model delta sigma weight residual 112.04 105.42 6.62 1.40e+00 5.10e-01 2.23e+01 angle pdb=" N PRO C 320 " pdb=" CA PRO C 320 " pdb=" C PRO C 320 " ideal model delta sigma weight residual 111.13 117.49 -6.36 1.49e+00 4.50e-01 1.82e+01 angle pdb=" N TYR B 158 " pdb=" CA TYR B 158 " pdb=" C TYR B 158 " ideal model delta sigma weight residual 109.69 114.96 -5.27 1.44e+00 4.82e-01 1.34e+01 angle pdb=" O LYS b 206 " pdb=" C LYS b 206 " pdb=" N ASN b 207 " ideal model delta sigma weight residual 123.29 118.98 4.31 1.18e+00 7.18e-01 1.33e+01 angle pdb=" N ASN b 207 " pdb=" CA ASN b 207 " pdb=" C ASN b 207 " ideal model delta sigma weight residual 108.18 100.84 7.34 2.01e+00 2.48e-01 1.33e+01 ... (remaining 22462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 8960 17.65 - 35.30: 732 35.30 - 52.95: 122 52.95 - 70.59: 37 70.59 - 88.24: 15 Dihedral angle restraints: 9866 sinusoidal: 4046 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 177.34 -84.34 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -143.76 57.76 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA TYR B 158 " pdb=" C TYR B 158 " pdb=" N GLY B 159 " pdb=" CA GLY B 159 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1853 0.047 - 0.093: 396 0.093 - 0.140: 134 0.140 - 0.186: 2 0.186 - 0.233: 2 Chirality restraints: 2387 Sorted by residual: chirality pdb=" CA VAL B 78 " pdb=" N VAL B 78 " pdb=" C VAL B 78 " pdb=" CB VAL B 78 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL B 78 " pdb=" CA VAL B 78 " pdb=" CG1 VAL B 78 " pdb=" CG2 VAL B 78 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA VAL C 25 " pdb=" N VAL C 25 " pdb=" C VAL C 25 " pdb=" CB VAL C 25 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 2384 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS b 206 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C LYS b 206 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS b 206 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN b 207 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 280 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO C 281 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 281 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 281 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 24 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASN C 24 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN C 24 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 25 " 0.010 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1073 2.74 - 3.28: 14674 3.28 - 3.82: 24917 3.82 - 4.36: 32176 4.36 - 4.90: 56207 Nonbonded interactions: 129047 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" OH TYR A 331 " model vdw 2.195 3.040 nonbonded pdb=" O ASP b 23 " pdb=" OG1 THR b 27 " model vdw 2.236 3.040 nonbonded pdb=" OG SER C 297 " pdb=" O TYR C 331 " model vdw 2.278 3.040 nonbonded pdb=" OG SER c 297 " pdb=" O TYR c 331 " model vdw 2.279 3.040 nonbonded pdb=" O CYS c 143 " pdb=" NH2 ARG c 148 " model vdw 2.279 3.120 ... (remaining 129042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'C' selection = (chain 'a' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'b' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.140 Find NCS groups from input model: 0.730 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: 0.010 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16576 Z= 0.166 Angle : 0.571 9.243 22467 Z= 0.311 Chirality : 0.042 0.233 2387 Planarity : 0.003 0.048 2865 Dihedral : 13.554 88.243 6038 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.23 % Allowed : 0.40 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.18), residues: 2022 helix: 0.89 (0.39), residues: 218 sheet: -1.81 (0.24), residues: 501 loop : -1.14 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS C 26 PHE 0.015 0.001 PHE B 160 TYR 0.009 0.001 TYR B 77 ARG 0.004 0.000 ARG b 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 331 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.6974 (m-90) cc_final: 0.6771 (m-90) REVERT: A 73 ASN cc_start: 0.7450 (m110) cc_final: 0.7241 (m-40) REVERT: A 136 ASP cc_start: 0.9059 (m-30) cc_final: 0.8749 (m-30) REVERT: A 154 GLU cc_start: 0.8845 (pt0) cc_final: 0.8639 (pt0) REVERT: A 240 GLN cc_start: 0.8740 (mm110) cc_final: 0.8454 (mm110) REVERT: A 288 GLN cc_start: 0.8295 (pt0) cc_final: 0.8047 (pt0) REVERT: A 307 LEU cc_start: 0.8182 (tt) cc_final: 0.7982 (tp) REVERT: A 344 ASN cc_start: 0.6334 (m-40) cc_final: 0.5528 (p0) REVERT: A 345 MET cc_start: 0.7951 (mtm) cc_final: 0.7688 (mtp) REVERT: A 347 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7631 (pttp) REVERT: B 31 GLN cc_start: 0.7342 (mt0) cc_final: 0.6890 (tp-100) REVERT: B 62 ARG cc_start: 0.7580 (ptm-80) cc_final: 0.7342 (ttp-110) REVERT: B 168 TRP cc_start: 0.8129 (m100) cc_final: 0.7914 (m100) REVERT: B 216 SER cc_start: 0.9272 (t) cc_final: 0.8977 (m) REVERT: B 314 ARG cc_start: 0.6880 (ttm-80) cc_final: 0.6337 (ttm170) REVERT: C 7 SER cc_start: 0.8354 (t) cc_final: 0.7997 (m) REVERT: C 146 GLU cc_start: 0.6612 (mp0) cc_final: 0.6368 (mp0) REVERT: C 213 GLU cc_start: 0.7968 (tt0) cc_final: 0.7738 (tt0) REVERT: C 258 GLN cc_start: 0.7643 (tp40) cc_final: 0.7419 (tp40) REVERT: a 292 ASP cc_start: 0.7520 (p0) cc_final: 0.6865 (t70) REVERT: a 314 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7652 (ttm170) REVERT: b 274 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7171 (mt-10) REVERT: b 293 HIS cc_start: 0.7990 (p-80) cc_final: 0.7755 (p-80) REVERT: c 102 ARG cc_start: 0.6856 (mmt90) cc_final: 0.6222 (tpp80) REVERT: c 147 ARG cc_start: 0.7269 (ptt-90) cc_final: 0.7067 (ttp-170) REVERT: c 255 ASN cc_start: 0.8735 (t0) cc_final: 0.8523 (t0) REVERT: c 312 CYS cc_start: 0.7472 (p) cc_final: 0.7206 (p) outliers start: 4 outliers final: 1 residues processed: 334 average time/residue: 1.3266 time to fit residues: 488.3585 Evaluate side-chains 247 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN B 76 ASN B 207 ASN C 166 ASN C 208 GLN C 263 GLN b 208 GLN b 288 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16576 Z= 0.232 Angle : 0.550 7.459 22467 Z= 0.290 Chirality : 0.043 0.148 2387 Planarity : 0.004 0.052 2865 Dihedral : 7.292 103.691 2228 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.17 % Allowed : 9.21 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2022 helix: 1.05 (0.38), residues: 220 sheet: -1.32 (0.24), residues: 514 loop : -1.22 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 28 HIS 0.004 0.001 HIS A 195 PHE 0.013 0.002 PHE A 277 TYR 0.016 0.001 TYR c 256 ARG 0.004 0.000 ARG c 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 253 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7105 (m-90) cc_final: 0.6860 (m-90) REVERT: A 73 ASN cc_start: 0.7511 (m110) cc_final: 0.7280 (m-40) REVERT: A 208 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: A 240 GLN cc_start: 0.8731 (mm110) cc_final: 0.8469 (mm110) REVERT: A 258 GLN cc_start: 0.8359 (tt0) cc_final: 0.8153 (tt0) REVERT: A 279 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: A 340 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: A 343 GLU cc_start: 0.6616 (pp20) cc_final: 0.6362 (pp20) REVERT: A 347 LYS cc_start: 0.8027 (ptmt) cc_final: 0.7634 (pttp) REVERT: B 31 GLN cc_start: 0.7486 (mt0) cc_final: 0.7128 (tp-100) REVERT: B 170 LYS cc_start: 0.7962 (pttp) cc_final: 0.7522 (ptmm) REVERT: B 279 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: B 314 ARG cc_start: 0.6945 (ttm-80) cc_final: 0.6408 (ttm170) REVERT: C 146 GLU cc_start: 0.6683 (mp0) cc_final: 0.6426 (mp0) REVERT: C 213 GLU cc_start: 0.7950 (tt0) cc_final: 0.7684 (tt0) REVERT: a 51 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6440 (mt-10) REVERT: a 292 ASP cc_start: 0.7468 (p0) cc_final: 0.6843 (t70) REVERT: b 147 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.6991 (ttp-110) REVERT: b 293 HIS cc_start: 0.7990 (p-80) cc_final: 0.7725 (p-80) REVERT: c 33 LYS cc_start: 0.7630 (ptpt) cc_final: 0.7294 (pttp) REVERT: c 102 ARG cc_start: 0.6871 (mmt90) cc_final: 0.6371 (tpp80) REVERT: c 173 GLU cc_start: 0.8057 (pm20) cc_final: 0.7757 (mm-30) REVERT: c 312 CYS cc_start: 0.7674 (p) cc_final: 0.7294 (p) outliers start: 38 outliers final: 19 residues processed: 268 average time/residue: 1.4150 time to fit residues: 416.2857 Evaluate side-chains 242 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 71 ILE Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN C 208 GLN b 208 GLN c 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16576 Z= 0.410 Angle : 0.645 9.495 22467 Z= 0.335 Chirality : 0.046 0.148 2387 Planarity : 0.004 0.039 2865 Dihedral : 7.313 61.119 2225 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.42 % Rotamer: Outliers : 3.49 % Allowed : 11.89 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2022 helix: 0.84 (0.37), residues: 221 sheet: -1.30 (0.24), residues: 508 loop : -1.41 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 28 HIS 0.006 0.001 HIS b 254 PHE 0.017 0.002 PHE a 251 TYR 0.019 0.002 TYR B 256 ARG 0.004 0.001 ARG c 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 240 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7188 (m-90) cc_final: 0.6874 (m-90) REVERT: A 73 ASN cc_start: 0.7405 (m110) cc_final: 0.7161 (m-40) REVERT: A 208 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: A 214 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8219 (mtmm) REVERT: A 279 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: A 324 LEU cc_start: 0.8477 (mm) cc_final: 0.8168 (mm) REVERT: A 347 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7775 (pttp) REVERT: B 31 GLN cc_start: 0.7492 (mt0) cc_final: 0.7072 (tp-100) REVERT: B 170 LYS cc_start: 0.7955 (pttp) cc_final: 0.7732 (ptmt) REVERT: B 208 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: B 238 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: B 279 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: B 314 ARG cc_start: 0.6867 (ttm-80) cc_final: 0.6235 (ttm170) REVERT: C 146 GLU cc_start: 0.6680 (mp0) cc_final: 0.6443 (mp0) REVERT: C 213 GLU cc_start: 0.8003 (tt0) cc_final: 0.7683 (tt0) REVERT: a 41 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6506 (mtm180) REVERT: a 51 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6714 (mt-10) REVERT: b 147 ARG cc_start: 0.7186 (ttp-110) cc_final: 0.6679 (ttp-110) REVERT: c 33 LYS cc_start: 0.7533 (ptpt) cc_final: 0.7122 (pttp) REVERT: c 102 ARG cc_start: 0.6805 (mmt90) cc_final: 0.6314 (tpp80) REVERT: c 154 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: c 156 GLU cc_start: 0.7881 (tt0) cc_final: 0.7261 (tm-30) REVERT: c 173 GLU cc_start: 0.8097 (pm20) cc_final: 0.7774 (mm-30) REVERT: c 312 CYS cc_start: 0.7848 (p) cc_final: 0.7355 (p) outliers start: 61 outliers final: 27 residues processed: 270 average time/residue: 1.2637 time to fit residues: 379.0807 Evaluate side-chains 265 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 208 GLN b 288 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16576 Z= 0.284 Angle : 0.575 9.642 22467 Z= 0.300 Chirality : 0.044 0.137 2387 Planarity : 0.003 0.036 2865 Dihedral : 7.194 61.691 2225 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 3.54 % Allowed : 13.49 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2022 helix: 0.97 (0.37), residues: 221 sheet: -1.43 (0.25), residues: 478 loop : -1.40 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 28 HIS 0.004 0.001 HIS B 254 PHE 0.015 0.002 PHE B 160 TYR 0.018 0.002 TYR c 256 ARG 0.003 0.000 ARG c 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 230 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7085 (m-90) cc_final: 0.6794 (m-90) REVERT: A 73 ASN cc_start: 0.7408 (m110) cc_final: 0.7169 (m-40) REVERT: A 208 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: A 279 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: A 314 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7430 (ttm170) REVERT: A 324 LEU cc_start: 0.8430 (mm) cc_final: 0.8074 (mm) REVERT: A 347 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7784 (pttp) REVERT: B 31 GLN cc_start: 0.7395 (mt0) cc_final: 0.6905 (tp-100) REVERT: B 157 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7421 (t0) REVERT: B 170 LYS cc_start: 0.7952 (pttp) cc_final: 0.7709 (ptmt) REVERT: B 208 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: B 238 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: B 279 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: B 314 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6333 (ttm170) REVERT: C 146 GLU cc_start: 0.6630 (mp0) cc_final: 0.6398 (mp0) REVERT: C 213 GLU cc_start: 0.7994 (tt0) cc_final: 0.7677 (tt0) REVERT: a 41 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6532 (mtm180) REVERT: a 51 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6703 (mt-10) REVERT: a 287 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7958 (mm) REVERT: b 30 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6424 (tt0) REVERT: b 147 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.6959 (ttp-110) REVERT: b 184 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8608 (mtt) REVERT: c 33 LYS cc_start: 0.7539 (ptpt) cc_final: 0.7105 (pttp) REVERT: c 102 ARG cc_start: 0.6778 (mmt90) cc_final: 0.6280 (tpp80) REVERT: c 154 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: c 156 GLU cc_start: 0.7882 (tt0) cc_final: 0.7316 (tm-30) REVERT: c 312 CYS cc_start: 0.7692 (p) cc_final: 0.7281 (p) outliers start: 62 outliers final: 30 residues processed: 254 average time/residue: 1.3202 time to fit residues: 373.3253 Evaluate side-chains 260 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 71 ILE Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 49 optimal weight: 0.0670 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 70 GLN C 208 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16576 Z= 0.303 Angle : 0.580 9.968 22467 Z= 0.302 Chirality : 0.044 0.139 2387 Planarity : 0.003 0.034 2865 Dihedral : 7.186 61.860 2225 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 3.66 % Allowed : 13.89 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2022 helix: 1.03 (0.37), residues: 221 sheet: -1.45 (0.24), residues: 504 loop : -1.39 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 28 HIS 0.005 0.001 HIS B 254 PHE 0.016 0.002 PHE B 160 TYR 0.019 0.002 TYR c 256 ARG 0.003 0.000 ARG c 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 228 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7108 (m-90) cc_final: 0.6817 (m-90) REVERT: A 73 ASN cc_start: 0.7415 (m110) cc_final: 0.7171 (m-40) REVERT: A 184 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8477 (mtt) REVERT: A 208 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: A 258 GLN cc_start: 0.8302 (tt0) cc_final: 0.8049 (tt0) REVERT: A 279 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: A 324 LEU cc_start: 0.8480 (mm) cc_final: 0.8109 (mm) REVERT: A 347 LYS cc_start: 0.8140 (ptmt) cc_final: 0.7813 (pttp) REVERT: B 31 GLN cc_start: 0.7553 (mt0) cc_final: 0.7029 (tp-100) REVERT: B 33 LYS cc_start: 0.7449 (mppt) cc_final: 0.6939 (mtmt) REVERT: B 157 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7423 (t0) REVERT: B 170 LYS cc_start: 0.7968 (pttp) cc_final: 0.7744 (ptmm) REVERT: B 203 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8473 (mt-10) REVERT: B 208 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6853 (mp10) REVERT: B 238 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: B 279 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: B 314 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6363 (ttm170) REVERT: C 146 GLU cc_start: 0.6623 (mp0) cc_final: 0.6390 (mp0) REVERT: C 213 GLU cc_start: 0.7986 (tt0) cc_final: 0.7728 (tt0) REVERT: a 41 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: a 51 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6681 (mt-10) REVERT: a 287 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7949 (mm) REVERT: a 292 ASP cc_start: 0.7694 (p0) cc_final: 0.6947 (t70) REVERT: a 314 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7770 (ttt180) REVERT: b 147 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.7011 (ttp-110) REVERT: b 184 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8625 (mtt) REVERT: c 33 LYS cc_start: 0.7510 (ptpt) cc_final: 0.7073 (pttp) REVERT: c 102 ARG cc_start: 0.6794 (mmt90) cc_final: 0.6276 (tpp80) REVERT: c 154 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: c 156 GLU cc_start: 0.7875 (tt0) cc_final: 0.7334 (tm-30) REVERT: c 173 GLU cc_start: 0.8116 (pm20) cc_final: 0.7776 (mm-30) REVERT: c 312 CYS cc_start: 0.7669 (p) cc_final: 0.7271 (p) outliers start: 64 outliers final: 30 residues processed: 257 average time/residue: 1.3306 time to fit residues: 377.5590 Evaluate side-chains 262 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 70 GLN C 208 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.006 0.045 16576 Z= 0.376 Angle : 0.622 10.530 22467 Z= 0.323 Chirality : 0.045 0.143 2387 Planarity : 0.004 0.033 2865 Dihedral : 7.317 60.703 2225 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 4.06 % Allowed : 14.92 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 2022 helix: 0.94 (0.37), residues: 221 sheet: -1.53 (0.24), residues: 509 loop : -1.46 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 28 HIS 0.005 0.001 HIS B 254 PHE 0.016 0.002 PHE B 160 TYR 0.021 0.002 TYR c 256 ARG 0.004 0.000 ARG c 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 229 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7105 (m-90) cc_final: 0.6814 (m-90) REVERT: A 73 ASN cc_start: 0.7402 (m110) cc_final: 0.7149 (m-40) REVERT: A 184 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8466 (mtt) REVERT: A 208 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: A 279 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: A 347 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7850 (pttp) REVERT: B 31 GLN cc_start: 0.7568 (mt0) cc_final: 0.7078 (tp-100) REVERT: B 157 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7439 (t0) REVERT: B 170 LYS cc_start: 0.7981 (pttp) cc_final: 0.7724 (ptmt) REVERT: B 203 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8479 (mt-10) REVERT: B 208 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: B 238 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: B 272 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7759 (ttmt) REVERT: B 279 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: B 314 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6286 (ttm170) REVERT: C 146 GLU cc_start: 0.6642 (mp0) cc_final: 0.6408 (mp0) REVERT: C 213 GLU cc_start: 0.7996 (tt0) cc_final: 0.7739 (tt0) REVERT: a 41 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7831 (mtp85) REVERT: a 51 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6841 (mt-10) REVERT: a 292 ASP cc_start: 0.7667 (p0) cc_final: 0.7011 (t70) REVERT: b 30 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6498 (tt0) REVERT: b 147 ARG cc_start: 0.7339 (ttp-110) cc_final: 0.6973 (ttp-110) REVERT: b 184 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8610 (mtt) REVERT: c 33 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7000 (pttp) REVERT: c 102 ARG cc_start: 0.6847 (mmt90) cc_final: 0.6301 (tpp80) REVERT: c 148 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6425 (ttp-170) REVERT: c 154 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: c 156 GLU cc_start: 0.7846 (tt0) cc_final: 0.7331 (tm-30) REVERT: c 312 CYS cc_start: 0.7759 (p) cc_final: 0.7287 (p) outliers start: 71 outliers final: 38 residues processed: 264 average time/residue: 1.2777 time to fit residues: 373.6295 Evaluate side-chains 271 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 221 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 284 THR Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 109 optimal weight: 0.2980 chunk 194 optimal weight: 0.0870 chunk 121 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 208 GLN b 288 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16576 Z= 0.131 Angle : 0.489 10.388 22467 Z= 0.256 Chirality : 0.041 0.131 2387 Planarity : 0.003 0.030 2865 Dihedral : 6.876 64.554 2225 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.40 % Allowed : 17.04 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2022 helix: 1.37 (0.38), residues: 221 sheet: -1.16 (0.23), residues: 540 loop : -1.20 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 28 HIS 0.003 0.001 HIS A 181 PHE 0.019 0.001 PHE B 160 TYR 0.020 0.001 TYR c 256 ARG 0.002 0.000 ARG c 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7065 (m-90) cc_final: 0.6807 (m-90) REVERT: A 73 ASN cc_start: 0.7375 (m110) cc_final: 0.7145 (m-40) REVERT: A 208 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: A 279 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: A 347 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7766 (pttp) REVERT: B 154 GLU cc_start: 0.8107 (pt0) cc_final: 0.7872 (pt0) REVERT: B 208 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6820 (mp10) REVERT: B 238 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: B 276 ASP cc_start: 0.7804 (p0) cc_final: 0.7369 (t0) REVERT: B 279 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: B 314 ARG cc_start: 0.6989 (ttm-80) cc_final: 0.6343 (ttm170) REVERT: C 146 GLU cc_start: 0.6630 (mp0) cc_final: 0.6398 (mp0) REVERT: C 213 GLU cc_start: 0.7959 (tt0) cc_final: 0.7658 (tt0) REVERT: a 41 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7817 (mtp85) REVERT: a 51 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6646 (mt-10) REVERT: a 292 ASP cc_start: 0.7508 (p0) cc_final: 0.7042 (t70) REVERT: b 147 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7108 (ttp-110) REVERT: c 33 LYS cc_start: 0.7509 (ptpt) cc_final: 0.7101 (pttp) REVERT: c 102 ARG cc_start: 0.6872 (mmt90) cc_final: 0.6234 (tpp80) REVERT: c 154 GLU cc_start: 0.8112 (tt0) cc_final: 0.6987 (tt0) REVERT: c 156 GLU cc_start: 0.7813 (tt0) cc_final: 0.7312 (tm-30) REVERT: c 173 GLU cc_start: 0.8082 (pm20) cc_final: 0.7722 (mm-30) REVERT: c 255 ASN cc_start: 0.8879 (t0) cc_final: 0.8510 (t0) outliers start: 42 outliers final: 18 residues processed: 255 average time/residue: 1.2894 time to fit residues: 366.3900 Evaluate side-chains 250 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS B 70 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16576 Z= 0.160 Angle : 0.501 10.697 22467 Z= 0.260 Chirality : 0.042 0.132 2387 Planarity : 0.003 0.032 2865 Dihedral : 6.811 64.483 2225 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 2.29 % Allowed : 17.95 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 2022 helix: 1.39 (0.37), residues: 224 sheet: -1.08 (0.23), residues: 540 loop : -1.11 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS B 254 PHE 0.017 0.001 PHE B 160 TYR 0.020 0.001 TYR c 256 ARG 0.003 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 228 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7078 (m-90) cc_final: 0.6817 (m-90) REVERT: A 73 ASN cc_start: 0.7380 (m110) cc_final: 0.7154 (m-40) REVERT: A 184 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8440 (mtt) REVERT: A 208 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: A 279 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: A 340 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6057 (tm-30) REVERT: A 347 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7770 (pttp) REVERT: B 208 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6796 (mp10) REVERT: B 238 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8407 (mt-10) REVERT: B 276 ASP cc_start: 0.7790 (p0) cc_final: 0.7367 (t0) REVERT: B 279 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: B 314 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6356 (ttm170) REVERT: C 146 GLU cc_start: 0.6614 (mp0) cc_final: 0.6393 (mp0) REVERT: C 213 GLU cc_start: 0.7953 (tt0) cc_final: 0.7663 (tt0) REVERT: a 41 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7806 (mtp85) REVERT: a 51 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6704 (mt-10) REVERT: a 292 ASP cc_start: 0.7517 (p0) cc_final: 0.7038 (t70) REVERT: b 30 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6305 (tt0) REVERT: b 147 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7074 (ttp-110) REVERT: c 33 LYS cc_start: 0.7557 (ptpt) cc_final: 0.7044 (pttp) REVERT: c 102 ARG cc_start: 0.6854 (mmt90) cc_final: 0.6221 (tpp80) REVERT: c 154 GLU cc_start: 0.8109 (tt0) cc_final: 0.6982 (tt0) REVERT: c 156 GLU cc_start: 0.7780 (tt0) cc_final: 0.7262 (tm-30) outliers start: 40 outliers final: 20 residues processed: 251 average time/residue: 1.2295 time to fit residues: 342.1336 Evaluate side-chains 252 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 310 GLN b 70 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 0.042 16576 Z= 0.164 Angle : 0.508 10.713 22467 Z= 0.263 Chirality : 0.042 0.132 2387 Planarity : 0.003 0.036 2865 Dihedral : 6.789 64.507 2225 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 2.17 % Allowed : 18.58 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2022 helix: 1.43 (0.37), residues: 224 sheet: -1.21 (0.24), residues: 510 loop : -1.10 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.009 0.001 HIS A 84 PHE 0.017 0.001 PHE B 160 TYR 0.021 0.001 TYR c 256 ARG 0.002 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7071 (m-90) cc_final: 0.6815 (m-90) REVERT: A 73 ASN cc_start: 0.7382 (m110) cc_final: 0.7161 (m-40) REVERT: A 84 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.5916 (p90) REVERT: A 184 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8447 (mtt) REVERT: A 208 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: A 279 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: A 340 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: A 347 LYS cc_start: 0.8166 (ptmt) cc_final: 0.7790 (pttp) REVERT: B 208 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6789 (mp10) REVERT: B 238 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: B 276 ASP cc_start: 0.7791 (p0) cc_final: 0.7368 (t0) REVERT: B 279 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: B 314 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6364 (ttm170) REVERT: C 146 GLU cc_start: 0.6590 (mp0) cc_final: 0.6381 (mp0) REVERT: C 213 GLU cc_start: 0.7954 (tt0) cc_final: 0.7662 (tt0) REVERT: a 41 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: a 51 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6701 (mt-10) REVERT: a 292 ASP cc_start: 0.7496 (p0) cc_final: 0.7078 (t70) REVERT: b 147 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7074 (ttp-110) REVERT: c 33 LYS cc_start: 0.7563 (ptpt) cc_final: 0.7049 (pttp) REVERT: c 102 ARG cc_start: 0.6867 (mmt90) cc_final: 0.6232 (tpp80) REVERT: c 154 GLU cc_start: 0.8116 (tt0) cc_final: 0.6964 (tt0) REVERT: c 156 GLU cc_start: 0.7773 (tt0) cc_final: 0.7287 (tm-30) REVERT: c 173 GLU cc_start: 0.8091 (pm20) cc_final: 0.7730 (mm-30) REVERT: c 318 MET cc_start: 0.8215 (mmp) cc_final: 0.7948 (mmp) outliers start: 38 outliers final: 21 residues processed: 243 average time/residue: 1.3222 time to fit residues: 354.6806 Evaluate side-chains 249 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain c residue 22 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 5.9990 chunk 191 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 201 optimal weight: 0.3980 chunk 185 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 310 GLN C 35 GLN C 166 ASN C 263 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16576 Z= 0.168 Angle : 0.509 10.812 22467 Z= 0.263 Chirality : 0.042 0.130 2387 Planarity : 0.003 0.034 2865 Dihedral : 6.749 64.502 2225 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 2.06 % Allowed : 18.75 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 2022 helix: 1.50 (0.37), residues: 224 sheet: -1.21 (0.25), residues: 490 loop : -1.05 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 168 HIS 0.003 0.001 HIS A 84 PHE 0.017 0.001 PHE B 160 TYR 0.021 0.001 TYR c 256 ARG 0.002 0.000 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7068 (m-90) cc_final: 0.6814 (m-90) REVERT: A 73 ASN cc_start: 0.7388 (m110) cc_final: 0.7166 (m-40) REVERT: A 184 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8448 (mtt) REVERT: A 208 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: A 279 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: A 340 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: A 347 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7795 (pttp) REVERT: B 146 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6804 (mm-30) REVERT: B 208 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: B 238 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: B 276 ASP cc_start: 0.7792 (p0) cc_final: 0.7365 (t0) REVERT: B 279 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: B 314 ARG cc_start: 0.6991 (ttm-80) cc_final: 0.6463 (ttm170) REVERT: C 213 GLU cc_start: 0.7951 (tt0) cc_final: 0.7658 (tt0) REVERT: a 41 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7797 (mtp85) REVERT: a 51 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6696 (mt-10) REVERT: a 292 ASP cc_start: 0.7466 (p0) cc_final: 0.7069 (t70) REVERT: b 30 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6308 (tt0) REVERT: b 147 ARG cc_start: 0.7501 (ttp-110) cc_final: 0.7128 (ttp-110) REVERT: c 33 LYS cc_start: 0.7566 (ptpt) cc_final: 0.7056 (pttp) REVERT: c 102 ARG cc_start: 0.6881 (mmt90) cc_final: 0.6280 (tpp80) REVERT: c 154 GLU cc_start: 0.8125 (tt0) cc_final: 0.6960 (tt0) REVERT: c 156 GLU cc_start: 0.7746 (tt0) cc_final: 0.7247 (tm-30) REVERT: c 173 GLU cc_start: 0.8056 (pm20) cc_final: 0.7737 (mm-30) REVERT: c 318 MET cc_start: 0.8174 (mmp) cc_final: 0.7882 (mmp) outliers start: 36 outliers final: 20 residues processed: 242 average time/residue: 1.2625 time to fit residues: 340.7256 Evaluate side-chains 245 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain c residue 22 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 5.9990 chunk 170 optimal weight: 0.0870 chunk 49 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 chunk 164 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS B 70 GLN C 263 GLN b 70 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.179140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122368 restraints weight = 16458.835| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.06 r_work: 0.2953 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16576 Z= 0.215 Angle : 0.536 10.887 22467 Z= 0.277 Chirality : 0.043 0.133 2387 Planarity : 0.003 0.035 2865 Dihedral : 6.823 63.647 2225 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 2.06 % Allowed : 18.93 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 2022 helix: 1.47 (0.37), residues: 224 sheet: -1.25 (0.25), residues: 490 loop : -1.09 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.003 0.001 HIS B 254 PHE 0.017 0.001 PHE B 160 TYR 0.021 0.001 TYR c 256 ARG 0.002 0.000 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6623.81 seconds wall clock time: 116 minutes 11.08 seconds (6971.08 seconds total)