Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 01:01:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/04_2023/7y66_33635_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/04_2023/7y66_33635.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/7y66_33635/04_2023/7y66_33635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/04_2023/7y66_33635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/04_2023/7y66_33635_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/04_2023/7y66_33635_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2097 atoms to isotropic. 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 59 5.16 5 C 5693 2.51 5 N 1517 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "S TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "E PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8917 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1795 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 6} Time building chain proxies: 4.75, per 1000 atoms: 0.53 Number of scatterers: 8917 At special positions: 0 Unit cell: (88.4, 119.85, 127.5, 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 59 16.00 O 1648 8.00 N 1517 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL E 7 " Number of C-beta restraints generated: 2128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 34.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.872A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.563A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.188A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.051A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 47 removed outlier: 4.877A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'D' and resid 35 through 67 removed outlier: 4.159A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 64 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 97 removed outlier: 3.964A pdb=" N TRP D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Proline residue: D 90 - end of helix removed outlier: 3.508A pdb=" N VAL D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 138 Proline residue: D 113 - end of helix removed outlier: 3.636A pdb=" N MET D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 151 through 173 Proline residue: D 170 - end of helix removed outlier: 3.789A pdb=" N LEU D 173 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 212 through 231 Processing helix chain 'D' and resid 239 through 267 Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 273 through 302 removed outlier: 3.811A pdb=" N LEU D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 4.155A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 301 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.646A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.783A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.719A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.986A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 221 through 223 removed outlier: 3.975A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.868A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.695A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.956A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.571A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 114 through 117 removed outlier: 3.721A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.250A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.636A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 175 through 180 removed outlier: 3.650A pdb=" N VAL D 176 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS D 185 " --> pdb=" O GLU D 180 " (cutoff:3.500A) 384 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: 2.39 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2874 1.35 - 1.47: 2248 1.47 - 1.59: 3903 1.59 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 9108 Sorted by residual: bond pdb=" C THR D 168 " pdb=" N ILE D 169 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.13e-02 7.83e+03 1.13e+00 bond pdb=" CA THR S 243 " pdb=" CB THR S 243 " ideal model delta sigma weight residual 1.528 1.555 -0.027 2.61e-02 1.47e+03 1.06e+00 bond pdb=" N ILE D 169 " pdb=" CA ILE D 169 " ideal model delta sigma weight residual 1.461 1.474 -0.012 1.23e-02 6.61e+03 1.02e+00 bond pdb=" CA THR B 164 " pdb=" C THR B 164 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.34e-02 5.57e+03 9.45e-01 bond pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta sigma weight residual 1.465 1.484 -0.019 2.03e-02 2.43e+03 8.94e-01 ... (remaining 9103 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.66: 202 106.66 - 113.51: 4983 113.51 - 120.37: 3371 120.37 - 127.22: 3690 127.22 - 134.07: 97 Bond angle restraints: 12343 Sorted by residual: angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N ILE D 169 " pdb=" CA ILE D 169 " pdb=" C ILE D 169 " ideal model delta sigma weight residual 108.88 114.36 -5.48 2.16e+00 2.14e-01 6.45e+00 angle pdb=" N ASP B 118 " pdb=" CA ASP B 118 " pdb=" C ASP B 118 " ideal model delta sigma weight residual 114.39 110.73 3.66 1.45e+00 4.76e-01 6.37e+00 angle pdb=" CA LEU S 178 " pdb=" CB LEU S 178 " pdb=" CG LEU S 178 " ideal model delta sigma weight residual 116.30 124.17 -7.87 3.50e+00 8.16e-02 5.05e+00 angle pdb=" CA MET S 192 " pdb=" CB MET S 192 " pdb=" CG MET S 192 " ideal model delta sigma weight residual 114.10 118.54 -4.44 2.00e+00 2.50e-01 4.93e+00 ... (remaining 12338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4976 17.49 - 34.97: 359 34.97 - 52.46: 45 52.46 - 69.95: 8 69.95 - 87.44: 8 Dihedral angle restraints: 5396 sinusoidal: 2099 harmonic: 3297 Sorted by residual: dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 188 " pdb=" CB CYS D 188 " ideal model delta sinusoidal sigma weight residual -86.00 -171.79 85.79 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CA PRO D 183 " pdb=" C PRO D 183 " pdb=" N PRO D 184 " pdb=" CA PRO D 184 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA TYR D 181 " pdb=" C TYR D 181 " pdb=" N PHE D 182 " pdb=" CA PHE D 182 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1062 0.045 - 0.090: 268 0.090 - 0.134: 65 0.134 - 0.179: 6 0.179 - 0.224: 1 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CB ILE D 169 " pdb=" CA ILE D 169 " pdb=" CG1 ILE D 169 " pdb=" CG2 ILE D 169 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 1399 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 89 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO D 90 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " -0.032 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO S 14 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 2 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO E 3 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 3 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 3 " -0.023 5.00e-02 4.00e+02 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 150 2.70 - 3.25: 8184 3.25 - 3.80: 13072 3.80 - 4.35: 16876 4.35 - 4.90: 29306 Nonbonded interactions: 67588 Sorted by model distance: nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.144 2.440 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.169 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.228 2.440 nonbonded pdb=" OD1 ASP D 282 " pdb=" NH1 ARG E 8 " model vdw 2.265 2.520 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.266 2.440 ... (remaining 67583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.970 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.002 0.035 9108 Z= 0.157 Angle : 0.585 7.865 12343 Z= 0.328 Chirality : 0.042 0.224 1402 Planarity : 0.004 0.050 1559 Dihedral : 12.302 87.435 3262 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1122 helix: 2.05 (0.27), residues: 377 sheet: 0.00 (0.30), residues: 287 loop : -1.66 (0.25), residues: 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.165 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 234 average time/residue: 0.9683 time to fit residues: 244.8168 Evaluate side-chains 199 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1575 time to fit residues: 1.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 346 ASN B 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9108 Z= 0.180 Angle : 0.550 7.611 12343 Z= 0.281 Chirality : 0.042 0.138 1402 Planarity : 0.004 0.047 1559 Dihedral : 4.191 34.267 1235 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1122 helix: 2.31 (0.27), residues: 378 sheet: -0.00 (0.30), residues: 292 loop : -1.54 (0.25), residues: 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 204 average time/residue: 0.9894 time to fit residues: 217.9745 Evaluate side-chains 212 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 8 residues processed: 13 average time/residue: 0.2156 time to fit residues: 5.2282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9108 Z= 0.206 Angle : 0.554 8.797 12343 Z= 0.285 Chirality : 0.042 0.131 1402 Planarity : 0.004 0.046 1559 Dihedral : 4.213 31.198 1235 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1122 helix: 2.37 (0.27), residues: 378 sheet: 0.11 (0.30), residues: 292 loop : -1.53 (0.26), residues: 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.053 Fit side-chains outliers start: 37 outliers final: 23 residues processed: 204 average time/residue: 0.9723 time to fit residues: 214.3949 Evaluate side-chains 217 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 9 residues processed: 16 average time/residue: 0.4982 time to fit residues: 10.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9108 Z= 0.187 Angle : 0.554 8.082 12343 Z= 0.283 Chirality : 0.041 0.138 1402 Planarity : 0.004 0.056 1559 Dihedral : 4.162 32.432 1235 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1122 helix: 2.42 (0.27), residues: 380 sheet: 0.22 (0.30), residues: 292 loop : -1.48 (0.26), residues: 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 0.940 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 200 average time/residue: 1.0041 time to fit residues: 216.8793 Evaluate side-chains 199 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 13 average time/residue: 0.3063 time to fit residues: 6.2241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9108 Z= 0.189 Angle : 0.546 7.605 12343 Z= 0.283 Chirality : 0.041 0.136 1402 Planarity : 0.004 0.057 1559 Dihedral : 4.195 36.431 1235 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1122 helix: 2.45 (0.27), residues: 380 sheet: 0.32 (0.30), residues: 296 loop : -1.37 (0.26), residues: 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 0.984 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 197 average time/residue: 0.9561 time to fit residues: 204.0866 Evaluate side-chains 199 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 8 average time/residue: 0.3206 time to fit residues: 4.4097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9108 Z= 0.234 Angle : 0.571 7.884 12343 Z= 0.295 Chirality : 0.042 0.146 1402 Planarity : 0.004 0.066 1559 Dihedral : 4.300 35.759 1235 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1122 helix: 2.36 (0.27), residues: 380 sheet: 0.34 (0.30), residues: 296 loop : -1.41 (0.26), residues: 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.019 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 201 average time/residue: 0.9720 time to fit residues: 211.4043 Evaluate side-chains 207 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 14 residues processed: 13 average time/residue: 0.3540 time to fit residues: 6.9748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 65 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 9108 Z= 0.143 Angle : 0.537 9.223 12343 Z= 0.276 Chirality : 0.041 0.139 1402 Planarity : 0.004 0.073 1559 Dihedral : 4.110 35.327 1235 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1122 helix: 2.48 (0.27), residues: 379 sheet: 0.49 (0.30), residues: 294 loop : -1.38 (0.26), residues: 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.048 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 193 average time/residue: 0.9480 time to fit residues: 199.2049 Evaluate side-chains 190 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1374 time to fit residues: 2.2999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9108 Z= 0.196 Angle : 0.552 9.685 12343 Z= 0.285 Chirality : 0.041 0.136 1402 Planarity : 0.004 0.078 1559 Dihedral : 4.181 35.441 1235 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1122 helix: 2.49 (0.27), residues: 378 sheet: 0.47 (0.30), residues: 296 loop : -1.36 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 0.956 Fit side-chains outliers start: 30 outliers final: 23 residues processed: 198 average time/residue: 0.9516 time to fit residues: 204.9350 Evaluate side-chains 201 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.3313 time to fit residues: 4.2806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9108 Z= 0.211 Angle : 0.567 9.827 12343 Z= 0.293 Chirality : 0.042 0.190 1402 Planarity : 0.004 0.082 1559 Dihedral : 4.209 35.586 1235 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1122 helix: 2.44 (0.27), residues: 379 sheet: 0.54 (0.30), residues: 294 loop : -1.37 (0.26), residues: 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.084 Fit side-chains outliers start: 21 outliers final: 20 residues processed: 194 average time/residue: 0.9146 time to fit residues: 193.0691 Evaluate side-chains 193 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.1687 time to fit residues: 2.3834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9108 Z= 0.163 Angle : 0.554 9.518 12343 Z= 0.285 Chirality : 0.041 0.202 1402 Planarity : 0.004 0.082 1559 Dihedral : 4.146 35.710 1235 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1122 helix: 2.49 (0.27), residues: 379 sheet: 0.55 (0.30), residues: 294 loop : -1.34 (0.26), residues: 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 0.943 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 197 average time/residue: 0.9744 time to fit residues: 207.6089 Evaluate side-chains 195 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1010 time to fit residues: 1.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115107 restraints weight = 12810.069| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.03 r_work: 0.3442 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9108 Z= 0.172 Angle : 0.558 9.251 12343 Z= 0.287 Chirality : 0.042 0.220 1402 Planarity : 0.004 0.085 1559 Dihedral : 4.150 35.843 1235 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1122 helix: 2.48 (0.27), residues: 379 sheet: 0.57 (0.30), residues: 294 loop : -1.33 (0.26), residues: 449 =============================================================================== Job complete usr+sys time: 3744.93 seconds wall clock time: 67 minutes 7.05 seconds (4027.05 seconds total)