Starting phenix.real_space_refine on Thu Feb 15 03:49:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/02_2024/7y66_33635_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/02_2024/7y66_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_33635/02_2024/7y66_33635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/02_2024/7y66_33635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/02_2024/7y66_33635_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y66_33635/02_2024/7y66_33635_neut_updated.pdb" } 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= 0.002 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-dev-5238/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: 4.91, per 1000 atoms: 0.55 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: 3.45 Conformation dependent library (CDL) restraints added in 2.0 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: 2.92 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: 2.07 Time building geometry restraints manager: 3.46 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 ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.35e+00 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 ... (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: 0.890 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: 0.000 Extract box with map and model: 3.810 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.900 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- 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= 0.158 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 % Allowed : 0.21 % Favored : 99.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS S 167 PHE 0.013 0.001 PHE B 199 TYR 0.022 0.001 TYR D 222 ARG 0.011 0.000 ARG B 197 *********************** 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 : 1.035 Fit side-chains REVERT: A 25 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 198 MET cc_start: 0.7757 (ttt) cc_final: 0.7485 (ttp) REVERT: A 248 LYS cc_start: 0.7387 (mtmt) cc_final: 0.7106 (mtmm) REVERT: A 289 GLU cc_start: 0.7373 (mp0) cc_final: 0.7072 (mp0) REVERT: B 215 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5596 (tm-30) REVERT: B 228 ASP cc_start: 0.7103 (m-30) cc_final: 0.6710 (m-30) REVERT: S 83 MET cc_start: 0.7344 (mmt) cc_final: 0.6724 (mmt) REVERT: S 192 MET cc_start: 0.7636 (ppp) cc_final: 0.7228 (pp-130) outliers start: 0 outliers final: 2 residues processed: 234 average time/residue: 0.9688 time to fit residues: 244.4452 Evaluate side-chains 199 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain D residue 43 ILE 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: 0.7355 moved from start: 0.1025 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= 0.184 Angle : 0.544 7.736 12343 Z= 0.279 Chirality : 0.041 0.154 1402 Planarity : 0.004 0.047 1559 Dihedral : 4.269 34.325 1239 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.48 % Allowed : 13.34 % Favored : 84.18 % 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: 0.32 (0.25), residues: 1122 helix: 2.34 (0.27), residues: 377 sheet: 0.03 (0.30), residues: 291 loop : -1.55 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS S 167 PHE 0.013 0.001 PHE S 177 TYR 0.014 0.001 TYR D 258 ARG 0.010 0.000 ARG B 134 *********************** 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 225 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 197 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7477 (ttmm) REVERT: A 248 LYS cc_start: 0.7455 (mtmt) cc_final: 0.7234 (mtpp) REVERT: A 289 GLU cc_start: 0.7465 (mp0) cc_final: 0.7155 (mp0) REVERT: A 308 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: B 198 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8145 (mt) REVERT: S 192 MET cc_start: 0.7635 (ppp) cc_final: 0.7152 (ppp) outliers start: 24 outliers final: 19 residues processed: 208 average time/residue: 0.9894 time to fit residues: 222.5848 Evaluate side-chains 216 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7383 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9108 Z= 0.221 Angle : 0.557 7.991 12343 Z= 0.287 Chirality : 0.042 0.153 1402 Planarity : 0.004 0.052 1559 Dihedral : 4.356 31.853 1239 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.52 % Allowed : 15.31 % Favored : 81.18 % 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: 0.40 (0.25), residues: 1122 helix: 2.38 (0.27), residues: 378 sheet: 0.11 (0.30), residues: 291 loop : -1.52 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS S 167 PHE 0.013 0.002 PHE S 177 TYR 0.017 0.001 TYR D 258 ARG 0.012 0.000 ARG B 134 *********************** 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 227 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7284 (mmmm) cc_final: 0.7005 (mttp) REVERT: A 25 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 197 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7561 (ttmm) REVERT: A 248 LYS cc_start: 0.7459 (mtmt) cc_final: 0.7223 (mtpp) REVERT: A 308 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: B 16 ASN cc_start: 0.8040 (m110) cc_final: 0.7663 (m110) REVERT: B 164 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8047 (m) REVERT: S 192 MET cc_start: 0.7633 (ppp) cc_final: 0.7301 (pp-130) REVERT: S 245 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7783 (tp) outliers start: 34 outliers final: 23 residues processed: 202 average time/residue: 0.9929 time to fit residues: 216.4719 Evaluate side-chains 215 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain S residue 246 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.7365 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9108 Z= 0.163 Angle : 0.537 7.715 12343 Z= 0.275 Chirality : 0.041 0.144 1402 Planarity : 0.004 0.053 1559 Dihedral : 4.183 36.907 1235 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.10 % Allowed : 17.06 % Favored : 79.83 % 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: 0.52 (0.25), residues: 1122 helix: 2.44 (0.27), residues: 380 sheet: 0.19 (0.30), residues: 291 loop : -1.44 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS S 167 PHE 0.012 0.001 PHE S 177 TYR 0.014 0.001 TYR D 174 ARG 0.013 0.000 ARG B 134 *********************** 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 210 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7274 (mmmm) cc_final: 0.7034 (mttp) REVERT: A 25 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 197 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7557 (ttmm) REVERT: A 248 LYS cc_start: 0.7409 (mtmt) cc_final: 0.7191 (mtpp) REVERT: A 308 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: B 16 ASN cc_start: 0.8053 (m110) cc_final: 0.7677 (m110) REVERT: B 164 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7968 (m) REVERT: S 192 MET cc_start: 0.7597 (ppp) cc_final: 0.7197 (pp-130) REVERT: S 245 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7873 (mp) outliers start: 30 outliers final: 22 residues processed: 192 average time/residue: 0.9569 time to fit residues: 198.8740 Evaluate side-chains 208 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain S residue 246 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7437 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9108 Z= 0.352 Angle : 0.616 8.317 12343 Z= 0.320 Chirality : 0.045 0.171 1402 Planarity : 0.004 0.058 1559 Dihedral : 4.488 35.105 1235 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.24 % Allowed : 16.65 % Favored : 79.11 % 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: 0.43 (0.25), residues: 1122 helix: 2.27 (0.27), residues: 380 sheet: 0.27 (0.30), residues: 294 loop : -1.50 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS S 167 PHE 0.017 0.002 PHE D 75 TYR 0.023 0.002 TYR D 258 ARG 0.015 0.001 ARG B 134 *********************** 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 240 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.7423 (mtmt) cc_final: 0.7198 (mtpp) REVERT: A 289 GLU cc_start: 0.7587 (mp0) cc_final: 0.7260 (mp0) REVERT: B 16 ASN cc_start: 0.8091 (m110) cc_final: 0.7680 (m110) REVERT: B 164 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8107 (m) REVERT: B 261 LEU cc_start: 0.8225 (mt) cc_final: 0.7983 (mp) REVERT: S 192 MET cc_start: 0.7581 (ppp) cc_final: 0.7271 (pp-130) outliers start: 41 outliers final: 26 residues processed: 216 average time/residue: 0.9170 time to fit residues: 214.9444 Evaluate side-chains 222 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain S residue 246 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7406 moved from start: 0.1923 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= 0.212 Angle : 0.571 7.820 12343 Z= 0.293 Chirality : 0.042 0.146 1402 Planarity : 0.004 0.070 1559 Dihedral : 4.348 34.970 1235 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.93 % Allowed : 18.41 % Favored : 77.66 % 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: 0.56 (0.25), residues: 1122 helix: 2.41 (0.27), residues: 379 sheet: 0.34 (0.30), residues: 294 loop : -1.46 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS S 167 PHE 0.013 0.002 PHE B 199 TYR 0.017 0.001 TYR D 258 ARG 0.016 0.001 ARG B 134 *********************** 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 228 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7154 (mtpp) REVERT: A 289 GLU cc_start: 0.7577 (mp0) cc_final: 0.7291 (mp0) REVERT: B 16 ASN cc_start: 0.8074 (m110) cc_final: 0.7686 (m110) REVERT: B 164 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8031 (m) REVERT: B 188 MET cc_start: 0.8009 (mmp) cc_final: 0.7790 (mmt) REVERT: B 198 LEU cc_start: 0.8108 (mt) cc_final: 0.7879 (mt) REVERT: B 261 LEU cc_start: 0.8228 (mt) cc_final: 0.7997 (mp) REVERT: S 192 MET cc_start: 0.7546 (ppp) cc_final: 0.7230 (pp-130) REVERT: S 245 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 291 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (tt) outliers start: 38 outliers final: 27 residues processed: 207 average time/residue: 0.9183 time to fit residues: 208.0891 Evaluate side-chains 223 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain S residue 246 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 43 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9108 Z= 0.187 Angle : 0.553 8.226 12343 Z= 0.283 Chirality : 0.042 0.152 1402 Planarity : 0.004 0.052 1559 Dihedral : 4.223 34.484 1235 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.83 % Allowed : 19.03 % Favored : 77.15 % 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: 0.62 (0.25), residues: 1122 helix: 2.40 (0.27), residues: 380 sheet: 0.40 (0.30), residues: 294 loop : -1.40 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS S 167 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR D 258 ARG 0.012 0.000 ARG B 134 *********************** 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 228 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: B 16 ASN cc_start: 0.8071 (m110) cc_final: 0.7671 (m110) REVERT: B 82 TRP cc_start: 0.8428 (m100) cc_final: 0.8118 (m100) REVERT: B 164 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7947 (m) REVERT: B 188 MET cc_start: 0.8038 (mmp) cc_final: 0.7827 (mmt) REVERT: B 198 LEU cc_start: 0.8108 (mt) cc_final: 0.7842 (mt) REVERT: B 261 LEU cc_start: 0.8225 (mt) cc_final: 0.8000 (mp) REVERT: S 245 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7968 (mp) REVERT: D 291 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8364 (tt) outliers start: 37 outliers final: 26 residues processed: 208 average time/residue: 0.9486 time to fit residues: 213.3566 Evaluate side-chains 215 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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: 0.7370 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9108 Z= 0.165 Angle : 0.547 8.639 12343 Z= 0.278 Chirality : 0.041 0.161 1402 Planarity : 0.004 0.077 1559 Dihedral : 4.128 34.689 1235 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.62 % Allowed : 20.06 % Favored : 76.32 % 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: 2.50 (0.27), residues: 378 sheet: 0.50 (0.30), residues: 292 loop : -1.38 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR D 174 ARG 0.017 0.000 ARG B 134 *********************** 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 219 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7736 (mp0) cc_final: 0.7205 (mp0) REVERT: A 308 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: B 16 ASN cc_start: 0.8065 (m110) cc_final: 0.7666 (m110) REVERT: B 82 TRP cc_start: 0.8427 (m100) cc_final: 0.8126 (m100) REVERT: B 164 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7916 (m) REVERT: B 188 MET cc_start: 0.8025 (mmp) cc_final: 0.7796 (mmt) REVERT: B 261 LEU cc_start: 0.8212 (mt) cc_final: 0.7980 (mp) REVERT: S 192 MET cc_start: 0.7538 (ppp) cc_final: 0.7248 (pp-130) REVERT: S 245 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (mp) REVERT: D 291 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8365 (tt) outliers start: 35 outliers final: 26 residues processed: 200 average time/residue: 0.9382 time to fit residues: 203.3418 Evaluate side-chains 210 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7390 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9108 Z= 0.212 Angle : 0.584 11.618 12343 Z= 0.296 Chirality : 0.042 0.136 1402 Planarity : 0.005 0.081 1559 Dihedral : 4.246 37.328 1235 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.31 % Allowed : 20.89 % Favored : 75.80 % 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: 0.67 (0.25), residues: 1122 helix: 2.42 (0.27), residues: 380 sheet: 0.47 (0.30), residues: 294 loop : -1.37 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.002 PHE D 172 TYR 0.016 0.001 TYR D 258 ARG 0.019 0.001 ARG B 134 *********************** 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 214 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7749 (mp0) cc_final: 0.7204 (mp0) REVERT: A 308 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: B 16 ASN cc_start: 0.8073 (m110) cc_final: 0.7683 (m110) REVERT: B 82 TRP cc_start: 0.8433 (m100) cc_final: 0.8126 (m100) REVERT: B 164 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7946 (m) REVERT: B 188 MET cc_start: 0.8046 (mmp) cc_final: 0.7831 (mmt) REVERT: B 261 LEU cc_start: 0.8213 (mt) cc_final: 0.7975 (mp) REVERT: S 192 MET cc_start: 0.7555 (ppp) cc_final: 0.7266 (pp-130) REVERT: S 245 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7981 (mp) REVERT: D 291 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8370 (tt) outliers start: 32 outliers final: 24 residues processed: 198 average time/residue: 0.9454 time to fit residues: 202.7367 Evaluate side-chains 207 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 294 CYS 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: 0.0170 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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: 0.7378 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9108 Z= 0.182 Angle : 0.572 10.142 12343 Z= 0.290 Chirality : 0.041 0.139 1402 Planarity : 0.004 0.083 1559 Dihedral : 4.249 37.005 1235 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.41 % Allowed : 20.37 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 5.71 % 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: 2.45 (0.27), residues: 380 sheet: 0.54 (0.30), residues: 292 loop : -1.37 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE D 172 TYR 0.014 0.001 TYR D 258 ARG 0.020 0.001 ARG B 134 ********************** 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 214 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.020 Fit side-chains REVERT: A 229 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6287 (OUTLIER) REVERT: A 289 GLU cc_start: 0.7774 (mp0) cc_final: 0.7282 (mp0) REVERT: A 308 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: B 16 ASN cc_start: 0.8074 (m110) cc_final: 0.7678 (m110) REVERT: B 164 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7883 (m) REVERT: B 188 MET cc_start: 0.8047 (mmp) cc_final: 0.7812 (mmt) REVERT: B 198 LEU cc_start: 0.8182 (mt) cc_final: 0.7907 (mt) REVERT: B 261 LEU cc_start: 0.8198 (mt) cc_final: 0.7978 (mp) REVERT: S 192 MET cc_start: 0.7544 (ppp) cc_final: 0.7259 (pp-130) REVERT: S 245 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7975 (mp) REVERT: D 291 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8367 (tt) outliers start: 33 outliers final: 25 residues processed: 196 average time/residue: 0.9614 time to fit residues: 204.0216 Evaluate side-chains 210 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 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: 2.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.131672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113526 restraints weight = 12828.719| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.04 r_work: 0.3414 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9108 Z= 0.221 Angle : 0.592 9.936 12343 Z= 0.303 Chirality : 0.042 0.163 1402 Planarity : 0.005 0.086 1559 Dihedral : 4.348 37.041 1235 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.52 % Allowed : 20.58 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 5.71 % 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: 0.66 (0.25), residues: 1122 helix: 2.39 (0.27), residues: 381 sheet: 0.47 (0.30), residues: 294 loop : -1.37 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.007 0.001 HIS S 167 PHE 0.013 0.002 PHE D 172 TYR 0.016 0.001 TYR D 258 ARG 0.019 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.70 seconds wall clock time: 70 minutes 8.00 seconds (4208.00 seconds total)